1)Units can't use boarding parties.
The current ship-to-ship boarding parties would be fine though. Docking with an enemy ship in combat is pretty improbable, but getting to range 1 for short range pods makes sense with the same ingame mechanics.
2) Ships can't be cargo. Units can't carry cargo.
Instead, try reducing ground combat to 1 round, and adjust the balance towards hitpoints instead of damage on troops.
That way, many transports get to participate in the same ground combat, and a strategy of many small drops becomes practical.
3) If your tech tree runs out, then research dies totally, and you lose that part of the game.
If you want to having your techs max out after a few years, I reccommend leaving a lot of extra levels with diminishing returns.
At some point, races may decide its not worth keeping the research centers around for 1 point more damage on their guns every few turns, and start swapping the research for resource miners and capture ships.
4) No opinion.
5) Better make the planet creation really hard and slow going, though, with plenty of disadvantages in other areas...
Being able to fill out your systems would be a serious advantage.
6) There is no damage type for randomizing an atmosphere. You could use a planet buster/creator combo to randomize the planet type and atmosphere until you get one you like, though.
7) If you're going with the galactic decay theme, it fits.
Eventually the universe will die a heat death and the victor will be left with rubble to rule
8) I don't think that really fits the theme of destruction. It also makes for invulnerable "planets" unless you make ringbuster components.
9) AIs? None. Racial Tech Trees? From the sounds of it, two or three minimum, I'd guess.
10) Depends on the variety of infantry. If its just going to be one basic infantry, then the guy with more wins. (

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Infantry plus elite forces, and some tanks plus the specials would provide the nessesary variety, though.
Take a look at the troops in GritEcon (and feel free to use some of it).
Infantry dominates there mostly because they are inexpensive cannon fodder. Without the pricey tanks to back them up, your campaigns will be long and gruelling, though.
A typical medium-large ground combat there will see tens of dropships delivering 50-100 tanks and a few thousand infantry. Because of the hitpoint balance, the infantry take most of the hits like armor for your tanks. Because a successful ground campaign takes quite a while to grind across the surface, both sides get a chance to drop and/or build reinforcements, too.
