There certainly are far more iconic (and cooler) Pokemon that could take Jigglyballs' place...
Yeah, I'm sure a lot of people would bitch to no end about it if they did take her out. Probably be worse than when X wasn't in MvC3.
But my reasoning is what little of a fan base she has. I've yet to find anyone who said Jigglypuff was their favorite character on the game. It's not that she sucks.
The main thing I was looking at was this:
Roy was taken out - Same moves as Marth
Young Link was removed - Replaced with Toon Link due to Windwaker, etc.
Dr. Mario was removed - Too similar to Mario
Mewtwo - Basically same as YL, taken out for a more up to date Pokemon that has a stronger fan base.
Pichu removed - too similar to Pikachu.
Jigglypuff would only be taken out by a more up to date Pokemon with a similar appearance.