I played my first game as the Vasari earlier today and I found a few bugs and/or confusing mechanics with them (some are applicable to the other races, too).
1) The first bug is one that makes me never want to research phasic shields as Vasari again... When you research phasic shields, all the civilian buildings are set to autocast it if they are under attack, but once they cast it, they never turn off unless you go in and do it manually! This is problematic because you start losing income and research bonuses from phased out trade centers and research stations.
Because the cooldown for the phasic shields is pretty short, I think that they should automatically deactivate maybe 30 seconds after they stopped being attacked, or at least when there are no more hostiles in the gravity well.
2) Another issue, which might not be a bug but seems like it, has to do with queued structures. It really bothers me that queued structures can be destroyed by enemies - it's both extremely annoying and very unintuitive. How can they blow something up that isn't even there? It makes trying to build structures while under attack really micro intensive and annoying.
Funny anecdote that leads to #3: I had just taken over a planet and queued 35 tactical and 20 logistical slots worth of buildings as Vasari, when all of a sudden a round from one of my Korath cannons that was fired half an hour ago from another star system hit the planet and took out the whole queue... AGH! I couldn't decide whether to laugh or cry

3) The superweapons. I think they're really fun - the advent's is my favorite. But I would personally prefer if either they couldn't shoot between star systems, or shoot faster projectiles. When there is a half-hour delay between launch and impact, it can lead to very undesirable results (see anecdote above). The advent don't have this problem, but the TEC have it even worse. Another thing I noticed is the superweapons don't seem to prioritize well by themselves. When I set them to autocast, they often fire at different solar systems when there are perfectly good targets just a few jumps away. They should always prioritize their own star system first, imo.
Edit: Thought of another thing that bothers me:
4) Giving commands to selections isn't always intuitive. For example, if I select 3 identical capital ships with an ability set /not/ to autocast, and right click the ability, it sets all three. But if I right click again, it only disables autocast on the sub selected unit. They should make this consistent! I also think that manually casting an ability shared by all units in a selection should make all the selected units act.
Additionally, you can't scuttle a whole selection - only the sub selected unit gets destroyed. In general, I think that a command that /can/ apply to a whole selection should.