I just played one game and this one issue was enough to make the experience quite sour.  Early in the game during a pirate assault on one of my planets one of their ships "disappeared".  It was no longer on the game map, but it was still listed as in the gravity well and the colony was still "under assault".  If I double-clicked the icon it would zoom in incredibly close and not let me zoom back out, the only way to do so was to double-click on another ship, but once I did the camera had shifted its pivot point to somewhere extreme and didn't act properly.  This was corrected with a restart of the game.
That's a small hiccup, but where things went bad was when it happened again with my Titan.  When it did I had the options of disassembling it or not taking the time to do so.  I selected it and tried to move it, tried to jump it, tried to attack with it, etc.  Nothing brought it back.
Both times the ships disappeared in normal game combat, but the only similarity would be the presence of a Kol, Sova, and the new kind of capital ship.  The makeup of the rest of the supporting fleet was different, and the first time it happened it was without the Titan.  As it seems to be random I am unable to repeat it.

Other feedback:
- Playing as TEC loyalists I was able to wipe an opponent out very quickly using Corvette-class ships and my starting capital ship at the beginning of the game.  They had already built planetary defenses and had a few capital ships.  This seemed to be an imbalance to me and, as a person who normally slow-plays, I don't know how I would defend against it.  Late game Corvettes were less effective but still have an incredibly high performance/cost ratio.
- The new capital ship appears to be very good, yet balanced.
- In the one game I played faction balanced seemed to be very fair, but I'll reserve final judgement until playing as Rebels.
- The visuals have been greatly improved, and things only even got a little slow when my giant corvette fleet got into a large battle.
- I appreciate the increase in number of ships able to be selected at once, I never hit the limit in the game. (although this might only be because of the way Corvettes are counted)