More:
One of the starbase point defense upgrades is named "CounterMeasureModule_Name".
The camera controls for viewing battles are impossible. Would be nice to see them improved.
Quick battles aren't as quick as I'd expect - it's still kind of tedious to wait for it to finish. Also, I'd appreciate an option to always use quick battles as the default.
Late-game starbase defense modules are kind of useless, even though the number of constructor modules required to fully arm a starbase is far higher than the number of modules for other bonuses. Seems like an area that suffers particularly from imbalance.
When assimilating or invading an enemy planet, often I want to change its focus entirely. Destroying all the buildings I don't need is more tedious than it needs to be. Can I have a bulldozer to just keep clicking on buildings I don't want instead of click on building -> click destroy -> next building -> etc?
On large maps it gets difficult to micromanage all of one's planets, but the governors are completely unsatisfactory for me. I can't specify things like tourism, trade, or influence focus; governors don't terraform; they don't seem to destroy obsoleted or unwanted buildings to make way for new ones that fit the focus better, which is most relevant for planets taken from an opponent; they don't seem to care very much about terrain or adjacency bonuses. Decent governor AI is surely a hard thing to get right, but I think it's too important to ignore. Especially because of how it would make AI less bad.
I feel like late-game weapon techs require a disproportionately high amount of research compared to late-game techs in other areas.
I'd have a lot of fun with tools for creating new tech trees and buildings and such for custom races. Doing it all by editing undocumented XML files is a terrible bore.
The auto explore option is kind of terrible. If I send multiple ships auto-exploring they'll usually just be right next to each other. If I send a surveyor auto-exploring I expect it to survey anomalies but it goes right past them.
AI colonizing a planet in the middle of my territory is both dickish and strategically pointless since it'll just be assimilated anyway.
Ships often have texture flickering when using symmetry and two of the same parts overlap.
I don't think it should be possible to assimilate planets which you haven't got the terraforming tech necessary to colonize them, and when invading the planet ought to be depopulated or otherwise damaged without the invader taking ownership.
I'd like a way to mod in random planet names and not just star names, "X I" and "X II" and "X III" get kind of boring after a while.