I feel like Mewtwo could beat Samus as well due to his insane telekinesis and him being one of the most powerful Pokemon in the series. Mewtwo is one of the few characters in the Smash roster in canon along with characters like Palutena, Ganondorf, Link, and Kirby that are like god tier level in canon.
I actually think Ness, and maybe Lucas would be stronger telepaths considering what Ness does in game. It also depends on if Samus has any sort of psychic blockers in the suit. Actually, since I think Lucas is actually a healer, he might could theoretically heal Dark Samus into nothingness too. It's an interesting theoretical interaction. Dark Samus is poison. Essentially a wound on the universe, so healing magics may theoretically hurt it.
I still say Palutena is overhyped just because she is technically a goddess despite Pit doing the heavy lifting and literally having to avoid killing her when they fight. I'd say her best feat is when she charges the canon at the end of Uprising, but even then, said canon is the equipment of a higher deity.
Link kind of depends on which Link we're talking about too. I also kind of like that Toon Link wasn't chosen to be a hero in so much as he chose himself. Still, the Hero of Time is probably one of the strongest Links...except the one in Smash is in kid form. BotW Link isn't a push over, but probably not the strongest, and he seems to be lacking any part of the Triforce. Meanwhile other Links, such as the first one, have at some point used the entire thing.
Let's be honest though, Sonic has a good chance of taking home the gold or at least the silver considering, as bad as the game might have been, he was crucial in defeating a being that existed in every moment of time at once. Yeah, he had help, but he was apparently critical to doing so. Not even Kirby did that. Though, to be fair as well, some of Kirby's threats seem kind of ambiguous as to if they match up to all the hype.
Then there's Bayonetta. Though, I think 2's final boss might be a bit misleading for some people.