My few cents:
Don't rearrange tech tree on trading/stealing
For starbase construction, automatically jump the focus to the last module type you built on the starbase - Making an Economy starbase with factories on it easier and faster to build.
Make more balanced super abilities - Abilities like Super Annihilator (Spore ships =

), Super Warrior (If you can destroy enemy ships in one turn, you don't need armor, and if you don't need armor you have more available firepower), so on, are incredibly good. Others aren't quite so good.
Add something, maybe in the scenario options, for turning on/off events. I personally would turn off stuff like the Jagged Knife event, but leave stuff like the Pirates.
More fleet bonus modules.
Auto-Repair modules for battleships, so that you can build a self-sufficient fleet of battleships.
Perhaps a 'Starbase Navigation' tech tree with long research times which increase the 4 starbase per sector limit.