Strange enough, the bad guys usually have a good reason to split up. Usually, the big bad is at the end of the road busy doing his thing, while his minions have their own territories and sub minions.
Only the good guys intentionally forgo teaming up just for the sake of forgoing it.
Er, no? Team battles are completely different from 1 vs 1s. Its inherent complexity is likely one of the main reasons manga/anime authors avoid it.