I'm more than fine with 2v2, but I can completely understand why it's disappointing to some. Between all of the possible team setups (and the synergy that can be composed within them), assists and just the sheer size of the roster(s), MvC2 and 3 are pretty much fighting game sandboxes (Maybe 3 moreso than 2). There's a ton of potential variety to be found in a 3v3 setup.
That said, Tatsunoko Vs. Capcom proved (to me, anyway) that the series can still be fun in a 2v2 format, and mixing in MSH Infinity Gem craziness should make for a good time. I'm not bothered, but I understand why some are.