I can't find myself saying that Geno and Mallow "don't fit the Mario canon" - we've seen characters in the RPGs who have full arcs or "emissary" style personalities (Paper Mario 64 and Super Paper Mario jump to mind immediately) and the baddies almost certainly are just as fitting as the random cadre of bosses you get in the platformers.
I don't think it aged that badly either. There's a sort of oddball humor to the game because it was originally translated by Ted Woolsey who didn't have a series bible for the Mario games. (Especially since a lot of the games humor in some places was derived from Japanese anime and stand-up comedy, so he had to invent certain things from whole cloth since the references are otherwise incomprehensible to a non-90s Japanese audience).
That said the game is definitely from a time before corporate brand management forced these characters to be stripped down to just their most basic personality traits. I'd say that's a good thing though.
It's just a really good game overall and it's easy to see how Paper Mario ended up evolving on these concepts and what's the good old "Square weirdness" that's only present here. Makes you wonder where things could've gone, had Square not moved FF7 development from the N64 to the PlayStation.