A few random things that bug me about this game:
The difference that luck makes in map generation is way too huge in my opinion, in one game you can start on a 5 planet system, with three or four immediately colonizable multi-planet systems with good starting planets and useful anomalies within range. In others you start with 1 or 2 planets in your home system, and find barely anything besides nearly uncolonisable systems (eg. barren, arid, lava, gas giant) or small systems in your immediate surroundings.
Luck in placement is just as important as actual skill as far as I can tell, which really bugs me (eg. in one game by turn 100 i had basically won, and had steamrolled all my enemies (who all got terrible starting positions), and had multiple 30 population systems which could build dreadnoughts which they couldn't even harm within three turns each. In another game I had 10 systems by that point and it took me 10 turns to build a cruiser at a planet, and was in a war I couldn't really win. Starting placement luck should make a difference, but the difference it makes is obsenely large in this game (although it will probably get ironed out).
The camera in battle annoys me, as well as the fact that it is very hard to tell the difference between ship classes (if they are side by side in the same battle its fairly easy, but if they aren't a dreadnought and a cruiser look largely the same).
Another thing that minorly bugs me is that you can build buildings that have no effect on your system (wheras they should just be invisible if they are totally useless).