Yay look I made a good suggestion =D

What I was thinking of, is seperating the teams at the start (so they can't kill one another) and then just throw them in one rather big destructable area (that is, spread out- JJ2 can handle a limited amount of destructable blocks so it will be a big level which isn't all that filled). After they have found the other team, points for the other team can be scored by killing an opponent and you can score a point for your team by falling out (teams should logically be of the same size because of this). When everyone is out, the team with the least points wins.

The level should function like this:
Scoring system:
-When the game has not been started yet, scoring points should be made impossible in any case by blocking the bases with triggered blocks that will be removed when the game starts. Just in case of lagginess.
-When warping players out of the level, they should pass the bases in the correct order to score a point (remember that points are bad- you score a point for your team when you die or fall out).
-When a player gets killed, the bases should be passed in this order too.

Start position system (tubes, triggers, mp-starts, both bases):
-if the game has not been started, put them in their team's pregame area (and set some triggers with trigger zones to make sure the player will pass the bases in the correct order after falling out).
-if it is a new player and the game has been started, put them in the circle-tube-with-gem-in-a-crate-thingy straight away.
-if it is a player that has died and the game has been started, let them score a point (by moving them over the bases in the correct order).

I could optimize my team GF 'level' and post a link here if anyone is interested.