Sakurai isn't dumb, he'd pull from the first 3.
See here's the problem.
Sakurai really doesn't have much to do with it. No matter which way it goes, it's Sakurai, he's a genius at moveset ideas which has been proven multiple time.
The problem is the most logical decision here. ssb as a series tries to reflect nintendo's franchises in a fighting game, that's prettu much the entire premise of the game. Now, that also means that if the franchises themselves were to change, changes should be made in ssb. Many existing characters got a lot of changes from ssbb because of this, new additions were also justified because of this. Now, sure, the characters may try to reflect the entire franchise history, but there's many many factor here, what is the most relevant about the franchise? What people are more aware about it? There's many factor that decides what would be a logical way to see a character.
But Paper Mario was never added in the game as of now and while ssb was moving on, the series changed drastically. So if they were to add him, it would only make sense to use the most recent representation because it has been changed since 5-6 years (add more because if they were to release a game on switch, likely add 3 years), not that the original one isn't relevant (in fact, pm64 was released in 1999-2000 so it's a pretty big streak of 3 games with the mario rpg idea), but this is such a change that it's impossible to overlook it.
So tbh, if Sakurai was to mostly consider the 2 lattest game, he wouldn't be dumb, it would be a logical decision.
EDIT: about the stage, this is a special case because I have no complains about it, at the time, the series had no representation so to have TTYD and ss was really the best, even I never expected a stage so I am actually happy about it.