According to the
Costume Mario page on MarioWiki, the Pikmin costume is right after the Olimar one, which would disconfirm this theory. Then again I don't know were there's a source for this...
We haven't seen any costume of Smash DLC character mostly likely because there's an embargo on which costumes may be revealed and which may not (remember those are review copies and reviewers are not authorized to reveal everything); for example someone shown the Dr. Mario costume but had to take it down because it wasn't authorized by the embargo. And still according to this MarioWiki page, there presumably are five slots between Pikachu and Olimar, so unless there's someone like Shulk or Chibi-Robo here I'd say it's pretty likely that the Mewtwo costume is in the base game especially considering his amiibo releases before the Animal Crossing ones.
At least I'm reassured about more costumes being promised through updates as long as more amiibos will release (though a source could be cool). I almost went paranoiac about the potential lack of DK costumes besides Donkey and Diddy (and DK Jr.) meaning that we weren't getting any DK character as Smash DLC