My first theory:
>Mewtwo, tournament mode, etc. patch
>Zard has new mega evo mechanics, Charizard X is his 3DS Final Smash, Charizard Y is his Wii U Final Smash, or vice versa
>Zard could also go X on Omega Stages and Y on regular stages, or X in 4 player smash and Y in 8 player smash, etc.
>Mewtwo operates on the same principles
My second theory is that Mewtwo X and Y are going to be two separate fighters, but those are very slim odds.
Overall, I don't think either theory will happen, most of all I'm hoping Roy is DLC alongside Mewtwo.
Roy could either be...
-A free character. If the off-looking leaks are anything to go by, he might be with the FE crew due to being free in a patch.
-A DLC character who appears with Mewtwo on April 9th or whenever Mewtwo's available early for Club Nintendo registrations.
-A DLC character who appears with Mewtwo when Mewtwo hits the eShop.
I haven't speculated this hard in a long time. It's really easy to hype this stuff when Roy might be closer than we think.