First I would love to see a private enterprise and civilian economy running in the background, a public AI controlled civilan trading vessels aswell as transports that would occupy the space of your empire. Some civilans could move from empire to empire trading and grouwing your own economy aswell. Don't forget the tax money you could get.

Nest are ground units that you train for battle on planets, things such as armour, infantry, and aerial units, or such would be fun to design or even just build and command instead of invading with civilian population forces. 

Last is something that should REALLY be added I would like to be able to colonize underwater through underwater domes, colonize space with better station mechanics and ontop of gas gaints in floating cities, would all be great and easilly do-able features. 

Anyways expand upon my ideas and ADD + your own.   Gal CIV 3 is great but there is so much more we as a community and the devs can all do to make it better than just a reskin of gal civ 2.

BTW love the new AI update. Really helps.