I dont know if anyone has already posted any of ths, but what the heck.
I liked the "modular ship design" idea, but only for the outward appearance, not for components. this otherwise defeats the kT-per-ship size principle.
Colony ships that *don't* disappear when you colonize. I mean, when you start, I can understand, but when you've got an empire the size of half the Galaxy, technology to flit between the stars in an instant, battleships the size of some of the larger asteroids, a population of over 3000 trillion and a monthly production that could actually be enough to buy Microsoft out, and you can still not use colony ships more than once? I mean, ever heard of Colony Drop Pods or something?
Colonist quarters that can carry only colonists, or people.
Separate storages for cargo types. I mean, you can store fighters in colony modules and population in fighter bays? C'mon!
More in-depth ground combat.
Things like Dropship Hangars or something - launch dropships (similar to fighters) from a distance to carry troops to the plant safely. say an enemy has got a massive amount of cap-ship-missile sats, you can sneak your dropships through their defenses. you just need to watch out for pdf cannons though
Ammo for things like missiles and depl-uranium cannons. you can't fire without ammo. Must also be coupled with the appropriate supply ships to resupply in space. Also handy for missile-pod fighters.
Resources that do NOT flit between the stars instantly, like they moved in another dimension or something... I mean, use auto-generated ships or custom-built ones to ferry your goods between the stars. Makes for interesting situations... blockades, pirates, loss of resources through disasters...
Actual travel time through warp points. For short ones (<100 ly), instantaneous, for larger ones, several turns to travel. Somewhat more realistic, and more interesting. Also, if you open a warp point from one side of the sector to another, this means your forces can't flit instantly towards something 500 ly away. Also, gives you nice options; a higher-level warp point closing device than can close warp points when ships are traveling through them... that way, if you've got only 1 system, and a massive enemy fleet is incoming, you can destroy it utterly simply by closing the warp point they travel through.
Racial tensions... ie if your race was at war with another for, say, 130 years and you force them to surrender and place their population on one of your worlds, your population gets angrier and angrier until the world erupts in civil war between the races and you need to send in ground troops to calm them down.
Covert contacts. If the enemy has captured your homeworld and relocated part of its population to make room for its own, you can contact your population on their planets and incite them to civil war or have them sneaking out of enemy territory and back to your planets.
Slave labor. Ie you capture enemy population and set them to work on, say, a very harsh desert world with massive mineral deposits. You then have them extracting the materials faster than usual, at the cost of some of their lives. You can set the scale of overworking on a slider.
Civilian weaponry. You can arm your civilians with varying degrees of weapons making them more effective in planetary defense - or civil war. Smuggle in weapons covertly to your opressed people, to allow them to capture the planet easily when you incite civil war.
Neutral or covert organizations, AI controlled. Like smugglers, pirates, mercenaries, espionage agencies...
Planetary raids (can also be on ships, bases) not to capture the planet but, say, perform an attack on enemy facilities to for example destroy facilities or construction queues, or to raid planetary warehouses for units or resources, destroy these things, or simply to abduct a part of the population - i.e. take them away as slaves.
Planetary surface use. This is not only for allotment of space for facilities/cargo/population, but can also mean that you have a huge sized planet with TWO colonies from different Empires. I mean, such a situation is very likely, don't you think? And this can also mean you can share Ringworlds and Sphereworlds.
Racial Events during gameplay. This can be a lot, for example;
-Primitive races inhabiting planets. You can have them work for you, take them all away as slaves, or obliterate them. Or, of course, you can colonize the planet and assimilate them into your society. This can be handy to gain extra bonuses, for example they may be Psychic or something, or they can even open whole new fields of research.
Primitives can be at the level of development of Amazone indians, or modern-day North America. This Last thing means thay can attack you with space-based missiles, nuclear or not, and that they may have sats or small space stations in orbit (think Mir or ISS). They might also have colonized their moon or a nearby planet.
-New races appearing at random. Some custom races state they were marooned in this sector by a warp point or a one-way colony mission, so why can't it happen during gameplay?
-Primitive races developing into space-faring Empires. At first they can be Neutral races, later they can develop into larger Empires.
-Neutral races venturing out of their system to become space-faring Empires.
You can also sometimes choose to start a game between highly-developed empires, making you dependent on trade and diplomacy for survival until you can make your move and secure your place as one of these larger Empires. That could also be your goal.
Start off as Neutral Empires or even primitives, while the rest starts out normally. Then you have to research certain things - think like "Steam Engine", "Flight" and "Particle Accelerators" to become a Neutral Empire, who then eventually needs to research something like "Interstellar Navigation" or something to exit your system and start plying the stars.
Missions. I.e. "quests" generated by the AI inside an empire, a neutral organization, or an Empire. For example, one of your planets might suddenly experience a Famine requiring you to ship a certain amount of Organics (dependent on planet size and population) for your citizens to stop starving and start loving you. This can be internal, but also external; the message might also be sent to another Empire. If that Empire then sends an Organics shipment there first, he gets control over the planet.
Or a player might create one saying, for example, "Whoever can close the Black Hole/destroy the Nebula/etc. in system [...] first gets 10000 Minerals and 25 high-tech Fighters." This could also be done in SEIV, but only to players you know, whereas an actual Mission might be sent to ALL players, AIs and neutral organizations.
Play as not an Empire but, say, an organization or a single ship! If you play, for example, a covert smuggler organization, you need to be able to produce and transport illegal goods, make connections with Empires, rebels or other organizations, and use this alternate form of diplomacy to win - or just to play on endlessly. Even if one empire destroys all the others, it could still be fun - smuggle goods for rebels, pirates, spies, trading organizations and the like.
If you play as a single ship, you need to be able to conduct diplomacy - transport goods on assignment, hunt down pirates or smugglers, join an organization or an Empire, trade in your ship (and a substantial amount of credits) for another (not one you design, unless you buy an independent Spaceyard, but one that is for sale - it may have been constructed, or sold by another captain-player, or it may have been captured... Your ship can be outfitted with all of the normal components. This means you can have a massive battleship, or a stellar manipulation vessel, a cargo ship, a boarding vessel, a minelayer, even a base. Some things are more exciting than others - piloting a battlecruiser is more diverse than keeping a resource-extraction vessel in orbit around a planet, and the former usually pays more, but is more dangerous. There is a far greater risk of getting killed when battling than there is when extracting resources, and you're not always assured with an assignment, however most empires would like to have a certain amount of resources per turn for a certain amount of credits, and you have a constant influx of money, not just one-time wads of cash.
You could also need to keep an eye on the morale of your crew; if you pay them more, they'll be happier, and when you deprive them of R&R for too long they will start complaining.
You can also buy Colony Ships, but they are extremely expensive - more expensive than a Starbase or a stellar-manipulation Baseship. When you have a Colony Ship, you can settle on a planet and start an empire of your own, which is when the gameplay changes from single-ship to Space Empire mode.
If this is too much like Starfury, oh well. But I don't think Starfury would allow you to start your own Empire.
Interplanetary/interstellar weapons!!!!! If you have interplanetary missiles, for example, you can initiate a bombardment of another planet from afar. You could even have a full-blown missile duel as guided or ballistic missiles are fired from and at two planets. Interstellar weapons would be even cooler; firing a missile that extinguishes a star from ten systems away is very handy. These missiles are similar to drones, only about the size of between Escorts and Cruisers and you could design them yourself. These missiles are not like drones, however, you select a target and then you lose control over them like you do over drones in battle.
You could also have planet-based weapons that aren't MDWs, but simply a means of obliterating an enemy ship three sectors away, or clearing an enemy minefield.
More components for Mines (and larger Mines). Like advanced cloaking devices to render mines even more difficult to see (coupled with better scanners) or something like a Self-Replication Unit. This would have to be larger than the second largest Mine and about 10-20kTs smaller than the size of the largest Mine. In ST
S9, self-replicating mines were used to lay a minefield in front of the Bajoran Wormhole. Each time a mine detonated, it was replaced by a freshly replicated new mine. These components need to be very expensive so you can't lay 500 self-replicating mines, and there needs to be a mines-per-turn limit, so that if a minefield with 100 of these mines is reduced to 10, you won't have 90 more mines in one turn. The limit should be as large as the number of remaining mines in the minefield, and no mines need to be replicated after one turn, so you won't have to forget about the minefields because they will grow back to original strength in a couple of turns. Also, no mines which have been cleared by Mine Sweepers will be created. This way Minesweepers are still useful.
More intel. DEFINITELY more intel.
More comprehensive intel.
Research projects that enhance a component or component type or several components. For example, "Small Ion-Rockets" would upgrade seeker missile speed (so crystal torpedos and space parasites don't benefit) and would extend the range of seeker missiles and Rocket Pods slightly.
More types of shields.
Something which allows modders to put in things like "hyperspace" or "warp drive" and sub-space communications (i.e. communications which cannot be intercepted/jammed/redirected/detected/etc.)
More types of random events.
A higher maximum limit for ships. MOST DEFINITELY a higher maximum limit for ships. I mean, if you've got an Empire that spans half the Galaxy and another one of the same size, wouldn't it be nice if you could have fleets of tens of thousands of ships fight against each other?
Fighters that can jump through warp points.
More types of vehicles/units.
Facilities which you can design - like weapons platforms, only then not with just weapons but also things like cargo space, resource extraction devices etc.
Nanotechnology. You can do so much with nanotechnology. Nano-storage is one thing - you can nanominiaturize objects so that you can store a helluva lot more on planets and in cargo bays, smaller components, sturdier ships, automated hull repair nanos built into all vessels which repair the hull and armor automatically but don't repair internal components, nano-jamming devices to disrupt the operation of nanotechnological devices...
If you build a ship/base, the empty hull is placed directly in space and then the components are created - like in SEIII. This would mean it would be handy to have repair in place at construction sites so large ships get done sooner.
Starship docking bays. In ST, starships can enter Starbases and dock inside. It would be nice to have a component like this in SE. Then, if you've got a Starbase around a planet, and it has a scanner jammer, an enemy might attack it unsuspectingly and suddenly face an entire fleet of starships.
Retreat from combat like in SEIII. In SEIV you can't cross the border of the combat sector, so you can't run away if one of your most vital convoys is attacked by an enemy Dreadnought which has just dropped out of cloak.
Cloaking during combat.
Reinforcements - i.e. ships with movement left around the battle sector can move into it to assist in combat.
Some sort(s) of valuable materials/money/standardised exchange rates/etc. like credits, Spice, gold, platinum, other sorts of rare metals yet to be discovered, etc.
Secondary material production. I.e. some planets can also produce other materials next to the standard resources - for example, mining stations can also mine things like titanium, Spice, etc. which will make production of certain objects cost less or which are required to be able to build certain objects in the first place, or which serve as money, etc. Farms can extract things like nitrogen, carbon, atmospheric gases etc. which can be used to, for example, make construction of atmosperic reprocessing facilities cheaper and which make the process Last shorter. Radioactive extractors can create rare isotopes that aren't your average Radioactive resources. If a mine mines uranium, for example, the uranium can be processed into the more effective material plutonium. You can also have things like Secondary Resource Processing Plants which can do nothing except extract and process secondary resources. This involves not only refining uranium into plutonium, but also things like creating alloys, prefabricate component parts for facilities or components, etc.
Pollution. I.e. you could have several types of resource extraction facilites. For example:
-The standard Mineral Mining Facility.
-An improved Version of the facility which extracts more resources but produces slight pollution.
-A large mine which produces very large amounts of minerals but which generates rampant pollution.
-The standard Organics Farm.
-Organics Growing Centers which grow more organics but which produce more waste in the form of organic and chemical residue and leftovers.
-Organics Extraction Centers which directly extract organics from across the entire planet but which totally obliterates the environment.
-Standard Radioactive Processors.
-Nuclear Reactors requiring uranium or plutonium which produce a far greater amount of radioactives but which cause large amounts of radiation.
-Large Nuclear Reactors requiring plutonium which can rapidly produce immense amounts of radioactives but which can reduce a paradise planet to a highly radioactive uninhabitable wasteland within three years.
Strip mining. Orbital ships which rapidly extract massive amounts of materials but which degrade the value immensely. You can only strip mine so much; then the planet is only a core, which will explode because of the energy generated inside. This will form an asteroid field.
Random events like the sudden collapse of moons or even planets, inhabited or not, into warp points, stars, storms etc.
Combat inside ships. Similar to planetary combat only then with marines. This would require the creation of more types of marines, but would make boarding action much more complicated.
Marine Infantry Troops which are strong on planets but even stronger on ships. They can be carried by ships to assist in boarding action or defense. You can design your own marine troops with things like body armor, zero-gravity armor, atmospheric insulation suits, assault rifles, demo charges, machine guns, plasma flamethrowers, etc. etc. etc.
Guerilla warfare. Covert operatives on enemy planets which can commit acts of sabotage, espionage and assault. This in accordance with the Covert Operatives I described.
Religion. You can have several levels of religious devoutness:
-Atheist; no religion
-Lightly Religious
-Moderately Religious
-Deeply Religious (the advanced trait should be renamed "Apllied Religious Beliefs" or something)
-Psychotic Devoutness (i.e. all other religions / levels of devoutness are heathens, and must be utterly exterminated)
This scale also influences the need for religious structures on planets. Lightly Religious people don't actually need much, though a planet with 5000M or more might require a minor centralized temple, Deeply Religious people will demand several temples of different types, which increase as the population grows, while psychotically devout people might actually want more than half of the planet's facility spaces filled with religious structures - like Temples, burial sites, meditation centers, religious educational facilities and so on. There can be several types of religion; large religions that have followers in several empires, smaller ones confined to a single one, religions that exist only on a single planet, etc.
More Advanced Traits that unlock tech areas.
More moddability... not possible, you might say, but I'd like to have the ability to renamy Minerals, Organics and Radioactives and would also like to be able to add new types of resources.
Tugboats.
Criminals/pirates/refugees/enemy spies/etc. and police/FBI-ish thing/Special Forces/etc.
More may be coming.