It's not 3v3. It starts out as 3v3, with revamped or changed abilities (not all ships, not all abilities), and the reinforcements will have new abilities just for coming into the battle, so it will wind up being 5v5 by the time the battle gets going. But with the changes in abilities (probably about half, plus all get a reinforcement ability), there will be a new dynamic as you have to decide who to use as a reinforcement and WHY you would use them at that time and not the other ship. It will be a totally different way of playing ships, but it will still be 5v5 after a few rounds.
