1) Create 2 new 'colony ships': Asteroid Mine and 'Cloud Colony' for asteroid belts and gas giants.
2) Give Anterians a scalable difficulty. Default would increase with difficulty, but player can select them to attack more often than the difficulty suggests. Also incurs a larger fleet at their homeworld.

I would add support for 32-bit and 64-bit OS's and to make the windows version run flawlessly....as in no errors when loading up.

I agree with these, plus

6. Ability to set up a default automatic queue for all new planets. Even if I had to go in and edit it as the game went along and tech improved, it would be nice.

7. Ability to remove or deactivate a weapon system in a captured ship (Who cares if I can't replace it). I screwed up all my treaties last game because I didn't realize the one captured ship in my fleet had Death Spores and I ran into a planet with a psychic system governor, so bombardment was required. Also the ability to keep a captured station.

8. The ability to make the same offers to the NPC as they can to me (start a tech trade offer, by offering something, ro requesting something)

9. Ability to either clean up a toxic planet, or blow it up and rebuild it as a Barren, without having to do the "Give away system/blow up own former colony/rebuild planet after reconquering the system" schtick.

10. Easier means of transferring colonists from system to system

#6 is one I beg to be included in all civ-type games.

#7 - of course there's nothing for it if you don't notice the weapon system, but it is of course possible to deactivate individual weapon systems on a battle-by-battle basis ... click twice on weapon system to turn it red, and forget about it for the rest of the battle. Just in case anyone reading this was unaware! (Clicking once prevents it from firing in the next volley only).

The problem was that this was on the Mind Control/Bombard screen - I had no access to individual weapons at that point

Oh, of course! I had stupidly overlooked that situation.

I would suggest, though, that rather than removing weapon systems, it would be preferable for the bombardment screen to allow one to choose to bomb, or use biological agents (as it now gives the bomb/mind control choice) - and likewise to stop them when one wishes (as it does for bombing). Then one could use one type of weapon, and if that doesn't achieve the desired result, consider using the other.