I think I was the only person who thought it was a good call to remove mewtwo. Not out of some weird spite, I just didn't think he fit. In the movies, Mewtwo was an untouchable god-like character. To have someone like jigglypuff or luigi fighting on par with him feels like a disservice to his character IMO.
That said I'll be glad if he returns just cos so many people want him back.
The only thing that should hurt Ganondorf is the Master Sword and light arrows yet Olimar throwing a pikmin at him can fuck him up.
In short the games aren't realistic measures of the characters powers and it's only for fun.