wat

but lucario and mewtwo were the interchangeable ones because of their similarity in roles/movesets (although sure once you delve into it they're really different)

Yeah, moveset wise, they are only similar in one aspect (NSpecial). Other similarities they share would be appearances, and the fact that they can both speak telepathically.

What.

No, Mewtwo was cut because of Sonic. Everyone in the roster was decided BEFORE development began, Sonic was added in later due to incredible fan demand. His inclusion killed the Forbidden 7 and his role in the subspace emissary shows how late he was added into development of the game.

Solid proof, please.

Just because sonic was added doesn't mean he took a slot that would have been filled by one of the forbidden 7. He was added late into development, most likely after the cuts had already been made. They didn't go "aw crap we need sonic, seeya mewtwo".

Mewtwo, and all of the other cut characters could have been cut for any number of reasons. Sakurai chooses not to elaborate as to the reason, maybe he has something planned for them. If he doesnt, then he doesnt.

Since they've gone and revived Mewtwo with the X/Y version, maybe Sakurai will think about bringing him back. Although, it might not be alongside Lucario, and a good reason to replace one, is to not have too much oversaturation of Pokemon characters. You never know, Mewtwo could just as well have been removed to make room for Lucario, and the Pokemon Trainer.

Also Sonic only got in because of fan demand, so I doubt that during the most of the developement, they kept his roster slot in the back of their heads.

Wait
of all characters, why would they put Pulse and Minum?

They were the Pikachus of their generations, akin to Pichu. That is one possible reason. They're also gimmick-ish pokémon so chances are the developers saw a chance to translate that into the smash engine for an original playstyle as well.

As a Gen III representative, I'd rather see Deoxys myself.

Pokemon is 2nd place as the one of the best selling video game franchises (Under the Mario franchise).
Logically, Pokemon deserves more reps as much as Mario's.

Mario, Luigi, Bowser and Peach.
Pikachu, Jigglypuff, Pokémon Trainer and Lucario.

They have the exact same number of reps.

Well, if we were including extra (Mario) characters like DK, Yoshi, and Wario.

We're not, since SSB (correctly) counts those as different series.

Well if you count Poke Trainer as 3 characters instead of one, since they kinda are 3 different characters, then Pokemon indeed has more reps than Mario.