With Marvel, it's because the MT Framework engine simply can't handle all the flashing lights and pretty colours, four characters being on screen at once, etc. It kinda breaks the game a little. Which, if I remember correctly, was one of the reasons Frank West wasn't in the MvC3 the first time. The engine couldn't handle all the zombies and stuff on the screen. If they made it for the 360 and ported it to the PS3, that makes sense. However, I've never noticed any slowdown on my fatty PS3.
It's kinda the same with SF and BB. Those run arcade perfect on PS3, but 1-2 frames faster on 360.
So, who knows?