Dr.Mario also sort of raises the question of why? With all of the new alt costumes happening why does Doc get a spot when he screams alt. Sure it could be a Lucina situation where he varies a bit but I don't know just seems strange
Dr. Mario is an established character with established functional differences to work off of, who was additionally a pretty popular character to play in Melee (and was quite a bit more popular than the character he was cloned from, unlike the other clones). He's actually quite an obvious choice when it comes to promoting an alt into a clone. Of course if Sakurai actually ignored the massive pleas to bring back Mewtwo, it would be a pretty dumb choice, as the fan backlash will be massive if Dr. Mario is back but Mewtwo isn't (even if Dr. Mario's inclusion has nothing to do with Mewtwo's exclusion). If Mewtwo is in though, fan backlash against Doc's return won't be that bad and mostly limited to those who'll complain about clones regardless.
Finally the big one why take Wolf and Lucas out for literally 2 other clones who by the way literally ascetically look the same to their clone originals. It's just so weird and dosnt seem right
Thing is, Lucas and Wolf almost certainly weren't taken out for the new clones, the process in development that those two got cut was different from when the alts were promoted. Current prevailing theory is that early on in development, Sakurai decided he needed to cut a few characters for whatever reason (probably space and/or time concerns). So he cut the Pokemon Trainer with Squirtle and Ivysaur, Lucas, and Wolf, deeming them the most expendable. Then later on, Sakurai sees space wasn't an issue after all or decides he can fit in a few more characters for whatever reason, but since Lucas and Wolf were cut early on, they have few or no existing assets to use (and they certainly weren't turned into alts when they differ so heavily from Ness and Fox), so Sakurai promotes a few alts into clones, as it would take barely any work (as opposed to recreating a semi-clone and a barely if at all semi-clone from almost scratch). Additionally, at this point, Sakurai also probably saw it would be better to just save Lucas and Wolf for DLC, where they can then be given proper attention and development time, rather than try rushing them back in almost non-changed and botching them in the process.
So as such, the clones can't be blamed for the exclusion of any character (besides other potential alt-to-clone characters).