It's actually very straight forward (not that its a position I hold), I've seen it expressed a few times, lemme boil it down.
Many, many, many people, specially life long Smash fans, have obscure nintendo reps they want in. The reason these characters are possible is because Nintendo/Sakurai has the spirit of representing all of Nintendo, everything from the big names to unknowns. As long as its cool and its Nintendo Sakurai will give it a shot.
Once you start focusing strongly on thrid parties, the number of big name third party reps possible will make the obscure Nintendo less important and likely. Why would they put in Isaac when they can just put in Cloud, stuff like that.
Big name third parties are a threat to these smaller Nintendo ips that people have been requesting for a decade.