That makes no difference. Shadow can be playable, but being third party only makes him unlikely. Mewtwo's time has passed, and adding him would make the a Pokemon franchise over represented, making him unlikely. Nintendo buying up SEGA on the other hand is highly likely, but Mewtwo's a lost cause.
It makes a big difference, because the rules for First Party inclusions differ vastly from Third Party inclusions.
Mewtwo has experienced a resurgence of prominence outside of Smash via being a poster boy for X&Y's Mega Evolution mechanic, while also having some meaty roles in Pokemon animated projects (Origins, the Mewtwo-Genesect movie, etc.). It's also clear that they're pushing the Mega Evolution mechanic in Smash as well, since now Charizard and Lucario possess their Mega Evolutions.
And Mewtwo is more significant within the Pokemon franchise overall than Jigglypuff ever was. He's really hot outside of Smash right now, so his "time" has most definitely not passed (though again, getting both him
and Jiggs is the preferable outcome).
Also, on what basis do you suspect, or expect, that Nintendo will purchase the SEGA company?