Well there's always the possibility that your pc isn't quite fast enough to run the game well.... mame has an emulation bug..... your video card and/or the filter you are using causes an almost inpercievable visual difference or some other random thing.
In general though, mame is identical to the real game. The few exceptions I can think of are vector games and games with an analog based sound system.
That doesn't guarantee that cps2 emulation is perfect enough though... I'm just saying in general.
The computer is waaaaaay beyond whats needed for CPS2, but I know what you were getting at. The picture looks identical and for all intents and purposes its the same, but it doesnt FEEL the same. Its not just Marvel VS Capcom, its Killer Instinct 1&2, NBA Jam, Open Ice, Kung Fu, BreakThru, Wresletfest, Mortal Kombat 2, UMK3,etc,etc .
I first noticed this "feel" thing with Neo Geo, when I converted my unwanted NeoGeo cab into a MAME for a coworker. I was playing Samurai Shodown II via MAME on the original neogeo sticks,buttons,layouts and it just wasnt the same.I dunno, its like generic cereal or something,lol