There's one very simple bug that's screwing up the team balance in pvp matches. Didn't take too much staring to figure out what's going on.
(Almost) everybody queues for two or three matches at a time, if they can't join one right away. The match starts when a certain number of people are queueing on each side, with the assumption that most of them will join.
When joining a match, you are not removed from the queue for any matches other than the one you joined. So, two thirds of the players queueing for any match have already joined a different match, were counted towards the quota for the next match anyway, will not be prompted to join the one which is starting, and the teams will start out short. The fix is simple: remove people from all queues when they join a pvp match (or other mission that will suppress pvp join prompts).
How about a quick fix on this one, guys? It should make pvp work better.