I quite like many of the quality-of-like interface improvements you've made. Keep it up!
I can order enemy fleets to undeploy as they're leaving their worlds(!)
I'd like a visual on where a battle is taking place before I decide whether or not to fight.
I was a bit annoyed by the need to setup my missile bases for every new planets before assigning defense sliders to build them, i think this should be optional in my opinion, as i don't remember in MoO1 having forgot to stop the defense slider when i didn't needed them, probably because i was never playing on the largest universe size.
Idea: Have a box in the colony screen for the default missile base target on new colonies, and have a button that sets existing to that number. Allow an infinite value (at -1, probably.)
It would be nice if using the mouse wheel to change planetary spending values aimed at larger amounts(dependent on how many items I can build) - Say, +1 pop each wheel click, or if I can make 100 destroyers, increments of 10.
When trying to move ships to a planet, it's annoyingly easy to select ships leaving it.
I should not be able to select planets and ships that are underneath the planet/fleet info box.
A bit of a gameplay question for once, when i play as Silicoids i found myself having a hard time to not having half of my systems rebelling on smaller universe and max opponents, so the Silicoid major advantage (not having to research special world environment to colonise them) isn't that big as you quickly run into opponent worlds that block your early spreading, the Silicoids have much more chances on larger universe settings.
Are you building pop with eco spending? I seem to be fine so far in my 50-star Silicoid game.