Part of me thinks it could be really interesting, while the other part of me thinks it could get pretty ugly in those types of matches. I don't think we'd be able to handle a 3v3v3 since 3v3 and 4v4 tend to get a little choppy as is.
But for a 2v2, do you still use the same scoring system for kills? This might restrict certain choices for ships, because you have to worry about your other enemy killing your current target. Which can lead to all sorts of rage and fighting between players (picture how mad people can get when even just allies steal their kills in other games). So disabling and balloon popping builds might not be as viable, forcing everyone to go the piercing/explosive route. (The time to kill for those builds is dramatically longer than for the piercing/explosive; allowing more time for someone to take your kill or just shoot you in the back).
What might work better in this situation is a score system change. Instead of getting points for killing, the team loses points for dying. This makes them care a lot less about kill steals, but more about staying alive. However, this can also influence ship builds, as teams may try taking out the 'softer' ships first, or encouraging everyone to bring the tougher to kill ships. (Something like 'stock matches' in fighting games; Super Smash Brothers anyone?) Whether is a 'team lives' or individual ship, although making it team could cause some in-team fighting when one ship dies over and over again, while the other stays alive longer.
And then you get the 4v2 scenarios, where 2 teams gang up on one of them. It might be two high level teams picking out the low level, or even two low level teams taking out the biggest threat (or maybe they just don't like pink). Overall I don't feel there's a bullet proof method of preventing this, and we'd just have to trust the players to be good sports.
