Basically convert the 3v3 to a 2v2v2. and maybe the 4v4 to a 2v2v2v2... maybe even free for all matches where ever ship for itself.. (I don't think free for all would be as good as having a team mate for various reasons).
Granted I know 3 team (or 4) would mean altering the UI to accommodate the third teams score and spectate mode info and spawns.. But aside from that I am not sure what else would need to be done.
I think the main benefit of this is it could lead to much more hectic matches.. Which.. Would mix stuff up a bit. I think it may benefit CP more then DM.
The draw back is.. 3v3/4v4 aren't known for filling up quickly as is and some people may not like it being more hectic..
As for team color.. Green and/or Yellow?.. They would probably be different from blue/red enough to know its not yours.
-maybe suggested before but not really sure how to search it-