I really liked it overall, but I think Shinobi is right. I would make it first to four wins in 45 minutes. That extra win (four, instead of three) helps teams who might not be as competitively based, but the time limit needs to be extended to give the losing team a better chance at making a comeback.
The KOTH style was very good for 3v3, and the giveaways for prizes in Ventrilo was a nice touch.
Since it's 3v3, though, I would put class limits on all the classes, and make it one of each class maximum. I don't think a team should be able to run multiple heavies or engineers, especially if they just win one round and are trying to turtle defend around the point for the remainder of the game. I think having one demoman, one sniper and one medic, for example, would make the games more fun, and it would increase everybody's desire to specialize in a class or two, instead of trying to play whatever is needed for a particular round.