Regarding the selection of capital ship abilities.
There is very little freedom of choice. In Rebellion you could upgrade abilities up to level 4 and the "Level 6 Ability" up to level 2. Now you are forced to do the same thing for every capital ship...all three standard abilities at level 3 and the final ability only has level 1.
I realize there may be a balancing argument to listen to, but I really feel like you should have more discretion in capital ship abilities. Even going beyond Rebellion's maximum of level 4 should be possible, you are focusing that ship's specialty on whatever ability you choose. Perhaps having your level 10 capital ship just have one ability upgraded 10 levels could even be doable (not the level 6 ability obviously, I am fine with that having just one or two levels). Again there would have to be some balancing, like if you go beyond a certain level the antimatter costs and cooldown times start increasing dramatically or something.
In summary, even Rebellion's simple addition of leveling an ability one more time, to 4, was liberating. Have two Akkans? One has colonize and the other doesn't and is free to blast away with its ion cannon (granted not an ability anymore). Now they both have to have colonize...
Also bring back the player portraits from Sins 1. I miss the almost "painted" quality of them, the depth of character and variety. They looked like an official portrait of your glorious leader. Where is my weird Advent turban-wearing entity and Vasari with big hat!
Anyway, I am enjoying the game so far. Perhaps I will voice more nitpicks in the future. I just had to get that abilities thing out in the air. Apologies if someone already brought this up.