Bugs are few at this point; most of the game was tested into total oblivion. And then the expansion caused the removal of even more.
Balance-wise, hmm, I cant speak too much for the solar map side of the game... I usually just play that on normal difficulty and can get a little lost in it every now and then (and the other 2 modes added in the expansion are balanced a bit differently). More familiar with the combat, I always have that on misery difficulty. For the base game the combat is fairly balanced though certain abilities are definitely OP, but not nearly enough to actually be a problem. I have a hard time judging the balance of the expansion's combat. I balanced out the stats on all the new ships as best I could, and tested them about a million times over, particularly as I kept tweaking and building upon the attack patterns they use (all of which are dramatically more complicated than the ships in the base game). But having seen only so much feedback on that stuff, it's hard to be certain that it's truly balanced, but I think it came out pretty well. The Obscura ships in particular are very nasty, with extremely complicated patterns on each one, which is exactly what Chris had wanted me to do with them. They came out well I think, but the mode that focuses on them wont be for everyone because of how hard they can get. Every pattern though is technically dodgeable, even in the game's turn-based format.
Now as for being able to affect things in the strategic side of the game, I'm guessing you had only played it pretty early on in the beta, when it was definitely a bit of a mess due to, well, it being early on in the beta. I think they did a wonderful job with it though in the end; there's a ton of different ways to approach different situations and you have ALOT of options. There's tons of different events and such that can happen too, spices it up nicely. It ended up being pretty darned complicated, but I think it's well balanced out. I havent seen any issues with the finished one myself, they seemed to iron out most of the issues by the time the base game released. Though again, I cant really speak for the higher difficulties on the strategic side; I actually find it pretty tough on normal as it is. But I do think they did a great job on it. If it's been awhile, I think it's worth a go, definitely. To me it's a pretty great game overall and I never found it dull at any point.
Of course, it's an Arcen game, so the usual tough learning curve is there, heh. Alot of experimenting is necessary. Something tells me that you dont really mind that aspect though.