Again, hopefully on the to-do list, but acquiring the ideology trait Cautious (4th rank of Vigilant on Pragmatic) is a HUGE PITA if you get it late in the game on Immense galaxies, as you end up with 3 separate ships sitting outside their colonies. When you have 100+ colonies, that makes for 20+ minutes of Fun getting them into orbit on the planets.
Could this be changed to (in order of my preference 
):
1. The ships start off actually guarding their planet, and not a hex away.
or 2. The ships are automatically in fleets when generated (reduce the clicking by a lot, at least)
or 3. If absolutely nothing else, generate the ships in order by planet and not by type, to avoid the camera panning around all 100+ colonies three times while the player does "right click the hex, smack enter for next Idle Ship" a lot.
I've also hit the "stuck with grayed out Wait" again, after Patch 2. It SEEMS to have been triggered by my clicking "Start" instead of "Auto Resolve" on two different battles (the question for the 2nd fight came up before the 1st one started), but not sure - it's the only odd thing I did that turn. Save and reload doesn't kick it loose either. I'll submit the save file to support.