In the Pokémon games, sure. But it doesn't have to be the same way in Smash Brothers.
Ganondorf could literally kill half of the cast in Smash Brothers very easily if he was in the Zelda games, but he doesn't in Smash (in fact a lot of the cast can KO him easily instead). His abilities aren't the same in Smash as they are in Zelda to make sure that the characters are (mostly) balanced and that they can be able to fight against each other without the one of them being seen as over powered, which basically makes your claim that people would only play as Mega Mewtwo Y crumble. You don't have to give Mega Mewtwo Y all of the perks it has in the game.
We argue that character canon isn't applied to Smash Brothers when it comes to supporting Ridley when we bring up Olimar, Kirby, Pikachu, Charizard, and Bowser's size. So in this case, Ganondorf's abilities (or even Mewtwo's in Melee as a better example) were not used to their fullest potential as shown in their game's canon. So why would this be changed now? If Sakurai wanted to make a Mewtwo that can switch forms to change how fast you move, how much you weigh, the damage of physical attacks, the damage of projectiles, etc. he'll do it. Hasn't stopped him from making Ganondorf swordless and poking fun at people who want him to use his sword.
And seeing as how you support Captain Ganondorf, I don't understand why you would question a character's moveset with their actual canon abilities.