Thank you so much for asking this question! JusDBerube, your efforts will not be forgotten!
None of the Pokemon from Brawl need to be cut and Mewtwo deserves to get back in. First off, Mewtwo is more or less seen as the original Pokemon villain, that doesn't mean much in actually getting into Smash, but to fans more villains and females brings diversity.
Mewtwo is a Pokemon icon! He was planned for Smash Bros 64, appeared in Melee, and was also planned for Brawl. He had lots of character data including things like specific victory themes present. He was far along and logic says if Sonic hadn't shown up out of the blue he would have made it in.
There will be a new Pokemon in this game, there is absolutely no doubt about that. So then why not Mewtwo? He is a beloved character of old school and new school players of Pokemon, not only that he can represent Pokemon X and Y with his new form as well.
Except for Pichu who was a last minute addition to literally pad the roster, each Pokemon that has appeared so far is worthy of returning.
Jiggly is a part of the original 12, it's coming back. Jigglypuff is cool and viable when you actually look past the simple looking move set.
Pokemon Trainer with the 3 original starters is such a nice concept for a character and the characters themselves are staples in the Pokemon world. While not impossible I do not see Sakurai cutting them for any current starters from X and Y or anything else in between.
Lucario has been the poster child for Pokemon since Diamond and Pearl. He did not replace Mewtwo in that sense of the word and his moveset is completely unique in animation and utility aside from 1 move, literally 1 move. He earned his place in the Pokemon world and there is no reason to leave him out of Smash 4.
Cutting characters for space is not a very good argument, shows me people just read headlines. The 3DS cards hold 8 GB correct? That is more than the dual layered Brawl actually used. As a matter of fact all 35 characters in Brawl only used 2 Gigs for character data. According to Sakurai, it's not the space that is causing trouble on the 3DS with characters, it is something more on the technical side with characters that transform and/are multiple characters. So I suppose Pokemon Trainer, Ice Climbers and the 2 women are in question.
Mario had 5 reps in Melee, no reason why Pokemon can't have 5 reps as well. It was intended for Brawl after all. I would argue with the popularity of each series, they both deserve it as well.
Rosters for Smash are decided so early, there is almost no way every character isn't already set in stone right now. Of course that is only going by previous history with this game and other fighters. I'm pretty sure Mewtwo is returning.
Thanks again JusD! You gave Mewtwo fans like me something to hang on to until Smash 4's release.