If team synergy is too valuable the choice wouldn't be between toons, but rather between teams of the strongest types of characters. And you run into problems where one or two of them is simply stringer than the rest. Compound that with chromium only characters and I shudder to think how off balance this could make the game.
I mean, it could be w perfect implementation, and it would be awesome. Or we could have a horrible overbalanced situation where f2p all make a nightsister team and all the p2p make a super Jedi team, and anyone not in those factions can cry in a corner.