Oh God... don't even mention it... I could go on for DAYS :insert smiley here, I ran out of smileys:
Just to start off the topic...
"Off-road" travel (move in interstellar space without using warp points)
Support for *.avi (or other animation format) in place of any *.bmp used in the game - probably unnecessary though if there is realtime 3D rendering!
Even more moddability, made possible by plugins - you don't like the resource system? Implement your own in any programming language you like, just make sure it links to the rest of SE5 using some standardized API - or maybe something like Stars! Supernova Genesis' "RDL" (Rules Description Language)
Realtime rendered ships & planets - yeah I know it's already in, but they're cool! (You say that cuts down on moddability? Just make it some standard format - most of us use some sort of 3D program or another, there's got to be a converter for Moray to DXF or whatever you use!)
Better sound effects!
Even SE4 Gold's "enhanced" sound effects, to be honest, aren't all that great
Some sort of prioritization system on the SitRep (stole that right off MOO3
it means the turn log) - color coding or different font sizes for different levels of urgency, perhaps? or filters - show only urgent Messages, etc.
Ability to order cloaked ships/units not to fight when they enter a sector containing enemies they can see, or those enemies enter their sector... annoying when those fancy unarmed spy satellites initiate combat with an enemy battlecruiser
Ability to queue orders in turn-based games - "I want you to load satellites here, drop them there, and repeat - oh crud the ship already executed its orders! now it won't repeat anything!
"
Planet Classification Schemes, like in MOO3 - give a planet up to 3 (or whatever #) designators such as "Mineral Rich", "Frontier", "Research Colony", etc. and have AI templates for facility construction on those types of colonies such as "Mineral rich colonies get 1 spaceyard, 1 robotoid factory, and the rest miners" or "Frontier colonies get" - the trouble would be to get the AI to reconcile planets with multiple classifications - what proportion of miners vs. research facilities vs. farmers
Facilities that take up multiple numbers of facility slots
Combination of facility slots, cargo space, and maybe even population space on a planet into "surface area" - you CAN have more defenses on a planet, but you have to sacrifice facilities or population, conversely you CAN make it a mega industrial complex but there won't be room for weapons platforms
Multiple spaceyards per planet!
Realtime 3D combat! :insert smiley here, I ran out of smileys: No really, I'm serious, they're doing it with MOO3 (well not the 3D part) - the way it works is, each of your fleets is divided into 1-8 taskforces, and the taskforces are what you actually control in combat, instead of piddling with the individual ships, which can be a pain when you have 100 ships on the battlefield! So early in the game, your TF's might be 1 escort, but later on your TF's could consist of, say, a troop transport with some heavy beam battlecruisers flanking it and PD cruisers on the edges of the formation. Then you just order the TF around - "attack enemy taskforce X" and they attack it, but each ship chooses its own target without having it manually specified. Sort of like a more advanced Version of SE4's "Formations"
Populations and facilities that actually consume resources! (Organics for most populations except mechanoids, none for autotrophs (populations that gather solar energy for food), and all resources for facility operation)
Custom moddable resources - you want Ironium/Boranium/Germanium instead of min/rad/org? You want "special resources" that are found only on rare planets and required to build exotic technology? You want to model every element known to man in the game so you need Titanium to build armor and Hydrogen for fuel cells? You got it!
Variable tech tree - like in MOO3 (a lot of my ideas are from there :insert smiley here, I ran out of smileys: ), just because it says you need level 12 Particle Physics to get Phasors doesn't mean you'll actually get it then - there's a random factor and you might actually get Phasors at level 11, or level 14!
Ability to put multiple damage types on a weapon so it can be 1/2x to shields but once it pierces the shields it's armor piercing, or damages only engines - some sort of checklist in the data files like "Damages shields? Yes, how much? 50% of normal? OK, how about armor? Oh, it skips armor...
Component/facility/unit(?) mods (generalization of weapon mounts) that modify any ability of a component, specified by name - "This mod increases the 'Firing rate' of your weapons, cutting it in half. (Works best with real time combat :insert smiley here, I ran out of smileys
And this one doubles the 'Cloak level' of your stealth devices..."
Firing Arcs and Shield/Armor/Component Arcs!!! My phasor can only fire 90 deg. forward and I'm shooting from an angle of 325 deg. relative to your cruiser, so I'm going to hit a hole in your shield and probably hit your engine, since it's on the left!
Real leaky shields/armor - my shield has an 80% deflection ratio, meaning that on average, 20% of shots will pass right through! (or maybe 20% of each attack will penetrate)
Something I've always wished for in a space game - the "Lego" ship design model! (I believe I suggested this when SE4 was in development :insert smiley here, I ran out of smileys
Basically what it is is, your ships are designed modularly - you simply drag components onto a grid, where each component must be connected to another component at specified connection points. Each component has a size and shape in grid squares, so a laser gun might be a 3x3 square with a 5-square line projecting from one side, while an internal component like life support could be represented by a simple block. Each component would also have a weight, which may or may not be proportional to its size (a 20 kT cargo bay will be mostly empty space so it's larger than a 20kT meson bLaster). Then various calculations are done on the ship to determine its vital statistics - a to-defense bonus/penalty could be calculated from the overall size of the ship in grid squares, for instance, while the ship's acceleration would be the thrust provided by the engines divided by the mass. (Could even have retro thrusters for backwards movement and rotational thrusters for turning...) Then, when the ship is damaged from some particular direction, the components on that side are hit first. Of course, this is probably more trouble than it's worth to begin with, both from a programming and a gameplay perspective
More realistic/sophisticated planetary habitability and sensor models - take a look at
http://sourceforge.net/docman/display_doc.php?docid=4154&group_id=17579 I cooked up for the "Universe" project - hey, even something like the temp/grav/rad model from Stars! would work, if atmosphere were thrown in as well!
Remote terraforming!
Planets, ships, and units of fairly continuously varying size - instead of planets being "Large", they would be "24,500 km" and population and storage capacity would vary as the square of the radius. Ships could be built in any size you want, with QNP (or even NP, for combat!) ratios calculated automatically, and shipsets would no longer be "this is an escort, this is a frigate" but instead there could be "lines" of ships (customizable in some text file of course) - standard ships, transports, carriers, colony ships, bases, etc. and your basic shipset would have pictures for various ranges in each of those categories - who needs a neostandard when you can say "this picture is for standard ships from 100-149 kT, this is for standard ships from 151-200 kT, etc." ... of course, this might play havoc with mods that change the basic component sizes for realism or sci-fi universe purposes - Aaah, I decreased the size of components, now all my ships look like escorts! :insert smiley here, I ran out of smileys:
Realistic unit sizes - 20 kT fighters are ridiculous! :insert smiley here, I ran out of smileys: How about modelling down to the ton on units?
That enough for a start? :insert smiley here, I ran out of smileys: