I believe Mewtwo would become DLC under the situation that they've already began working on it but never finished it, as I doubt they'd let their work go to waste. (Even though I'm making a lot of assumptions right now)
Although, one of the designers managed to squeeze in that extra Zero Suit Samus costume, so if Mewtwo wasn't one of the original characters to be included on the roster, I wouldn't underestimate their dedication to get Mewtwo in there.
Besides, these characters also go somewhat on popularity and demand, especially from Pokemon (This is why Charizard, Greninja and Lucario are all in the game). There is over a literal crap-ton (it's a measurement, apparently) of positives going for Mewtwo, with little to no reason not to have him.
It'd be more unfortunate than logical to not have Mewtwo, if you ask me. ("Unfortunate" includes things like time constraints, too, but I doubt that's going to happen.)
Even moreso, I'm pretty sure that the overall team dedication for this project is craaaaazy high compared to the previous 3, because of a couple of reasons (nowhere near every possible reason)
-Dual-console game
-Characters have been cut before due to restraints; pretty sure they wouldn't allow themselves to do that as easily again.
-(Synergizes with previous point) They'll definitely make sure to finish what they started.
Actually, with that third part being said, I believe the possibilities are that they're working on Mewtwo as we speak, have finished it already, or never decided on it in the first place. Although, reasoning can moreso point to the former possibilities. (I'm expecting to see some Mewtwo within the next 2 weeks)