For me, the order of the Pokemon on the CSS no matter what isn't going to make sense
Added to Smash order?
Pikachu, Jigglypuff, Mewtwo, Charizard, Lucario, Greninja
Mewtwo before Charizard seems weird in this order. Charizard bookending the Gen I Pokemon doesn't make sense beyond him being added after Mewtwo in the Smash games.
Pokemon order?
Charizard, Pikachu, Jigglypuff, Mewtwo, Lucario, Greninja
Pikachu not being first for Pokemon is bad
Smash 4 trophy order
Pikachu, Charizard, Lucario, Jigglypuff, Greninja, Mewtwo
What in the world? Gets all messed up because of Brawl Jigglypuff being a last minute addition and Mewtwo being DLC. It makes no sense at all. Seriously, there is no logical order to any of this beyond internal character index, which nobody really cares about.
"Feels right" order
Pikachu, Jigglypuff, Charizard, Mewtwo, Lucario, Greninja
Not really in any logical order, but it's the order that "feels" the best to me. It's sort of a mix of Smash order and Pokemon number order, only Charizard and Mewtwo are swapped from Smash game order, but it "feels" better having Mewtwo after Charizard. Everyone being lumped into generations is nice as well.
Then you throw Pichu in the mix for whatever reason, and things get super wacky because Pichu should be next to Pikachu. Or maybe between Mewtwo and Lucario in the "feels right" order. Actually that maybe would work