First off: great start on one of the most ambitious genre crossing I've witnessed to date. The background nebula look nice and give a nice look for the galaxy.
some things that caught my attention:
-rally points from capitol shipyards: when i set a rally in a neighboring system the capitol ships move to the edge of the building system and then sit there.
-warping large fleets and warping in general: at first it seemed a little off for the ships to be able to go to any edge of the gravity well and then jump out, but i got over that. Then main issue I have is when moving a large fleet with varying ship sizes it all breaks apart and just trickles in 1 ship after another. The option to have them all warp at the same time would be nice.
-collision awareness: fighters flying through structures happens frequently.
-diplomacy: i'm assuming at this point it really isn't that integrated yet, but it seems very hard to NOT shoot at non-aligned units even with auto fire off. Seems that there really isn't an option to increase your standing or favor with the other players except by leaving them alone. Having some kind of good-will option might be nice.
-construction frigates: there was a period when my home system (never got attacked) didn't have a constructor. When i saved and reloaded it was there.
can't think of anything else at the moment. Only had an hour or 2 with it. Good job so far, hope this helps!