I like autoreplace, remove some of the tedious fleet management.
Maybe shared artifacts could be a research or pact or some diplomacy option because i don't like that if my friend has an artifact that helps me a lot on a planet that he needs, then I have to either unally/have him give up the planet or loose out on the artifact.
It makes sense that if one empire is allied with another for them to share some technology.
The top of my wish list is 64 bit but i have no delusions of that happening in rebellion.
The thing i think they should work on first is the scale of the titans. the tec rebel titan feels like a large capital ship, hardly titanic in proportions. when i first heard about the titans, i expected them to be massive bunker busters that was a huge achievement to kill. Now I understand why they can't be as late game or as powerful as I initially thought, but i still think they should be bigger, especially the TEC titans.