It's an awesome game since you mentioned in the plan that you are open to suggestions for additions, these are mine:
Allow multiplayer with teams (perhaps up to 4 players on each team), this would be great for competitions.
Allow two players to play through the campaign. They control the same nation together, and control battles together.
Make the targeting computer allow you to specify parts of the enemy ship to aim at.
Allow others to spectate ongoing games
Introduce a built-in ranking system for ranked play (would be good with doubles play, etc. if more multiplayer was added).
Perhaps you could tell targeting computers to target specifically cockpits, suspendium, water storage, etc. But only if you've captured one of their ships before, because now you know the layout of that ship!
To compliment that idea, maybe instead of ordering Air Marines to capture a ship, you could order them to board an enemy ship and scout it, then jump back onto a friendly ship when it gets close enough.