When I open the Fleets toolbar and right-click a fleet, the camera instantly moves to that fleet. This is really annoying if I'm trying to select the fleet to tell it to "come here". I have to use the fleet hotkeys instead, which is ok, but I'd rather the right-click function worked like the hotkeys do - once to select the fleet, again to move the camera to it.
When I select a fleet, the "current selection" box in the bottom-right doesn't display the contents of the fleet. I know this is by design, but I can't figure out a way to make the current selection box instead display the units in the fleet, other than by getting it all in one place and selecting it. For example - I want to select all the v-wings in Strike Fleet Hostis. Ideally, I'd be able to open the Fleets panel, right-click the fleet to select it, then click a button to switch from "selected fleet" to "selected all units in fleet individually", then click on the V-wing section to just get those units.
...now that I think about it, the whole game is "left-click to select, right-click to issue orders" EXCEPT the fleet panel, where you right-click to select and left-click to make changes to the fleet. Changing it would confuse current players, though.
Similarly, I'd quite like a button that was "select the fleet that this unit is a part of". This might already exist but I don't know where it is.
Holding X and clicking the delete icon will delete units without the prompt, but holding X and pressing the delete key doesn't. And there's no way, as far as I can tell, to disable the "are you sure?" prompt for deleting units like you can with the one for upgrading tech.
I can collapse the left-side toolbar by clicking, say, Planet and then Planet again, but not by pressing P and then P again. Alternatively, just add a "collapse toolbar" hotkey. I'd use it all the time.
Right-clicking on the planet name in the top left instructs your units not to path through the planet if they can help it. However, as far as I can see, there's no visual indicator of this in the galaxy map or in the planet view. This seems like something that could cause problems if I do it by accident on a planet - I'd have no indication why my units were suddenly behaving stupidly! (EDIT: I see this is a new feature and you're intending to add a better indicator. Please do.)
I can't find the option to rename planets. Is there such an option? You could in AI War Classic, and I used it all the time to help me keep track of where interesting things were.
Opening the main menu clears my current unit selection. This is a bit of a nuisance.
There's no option to automatically pause when starting a new game like there was in AIWC.
Some of the nebula backgrounds are annoyingly bright. Is there an easy way to remove unwanted backgrounds from the list, or just make all of them a bit more subdued? I found the "reduce overall brightness" and "reduce overall saturation" options, but those affect everything else too.
The opposite is also a problem - with really dark nebula backgrounds, the asteroid belt is very hard to see. I'd like an option to draw a glowy circle instead of (or as well as) the asteroid belt.
In the Custom Setup screens, I'd like a way to collapse the "log" sidebar. It's usually not very helpful and just eats up screen real-estate that would be better spent displaying more of the map.