Hmm, you could also make team boss fight like this:
-Some predefined bosses in some predefined order will be spawned one after the other. New bosses may come in new rooms that were designed for that boss. All bosses should be much weaker than they are normally.
-After that a 'bonus round' begins, spawning a lot of normal enemies. After the bonus round, the bonus should be awarded. You'll need some kind of performance meter, possibly a timer, to determine the size of the prize. The bonus could include ammo, power ups, carrots and even one or two full energy carrots for very quick teams.
-Then, the bosses you defeated earlier will be spawned one after the other again, but this time with a higher difficulty.
-As the difficulty rises further, the rooms you are playing in may get harder by adding (or removing) walls, collapse/destruct/trigger scenery or even some normal enemies. You could also rise JJ2's internal difficulty setting, as it manipulates some bosses. Or at least one, as I know the queen boss works differently on other difficulty settings.