The main difference I've noticed with Falcon is just that Raptor Boost in PM becomes a valid recovery option. This is not the case in Melee. So in Melee, you'll be a little more already-dead when your CF is knocked off stage.
Ganon loses is side B choke move. In Melee it doesn't hit through shields or setup a tech chase. Way worse all around. And he doesn't have his float/reflect thing from 3.5 either, of course.
They probably also have a ton of less apparent, more important, more fundamental changes. Stuff like frames of lag after moves, knockback, percent dealt, etc. Both are worse in Melee for sure, but CF is the better of the two, and closer to his PM self.
Also, I very much agree with PM being more input lenient. Not sure what it is exactly changes. But there are things I can barely do or not do in Melee, then I try in PM and they just work.