So here is one thing I want to bring up.
Bayonetta.
She's a bit of a unique case as far as third parties are. The franchise is very small and while it was one of the must plays on the Wii U, it wasn't even a million seller.
For a third party choice, its unorthodox, but I have one idea that helps her make more sense.
Bayonetta 2 and 3 are partially owned and published by Nintendo. And certain franchises like this are treated and categorized differently in Smash.
For example, Shovel Knight was published by Nintendo in Japan.
www.destructoid.com
And the Shovel Knight spirits are sorted with the Misc. Nintendo spirits.
Rayman... has a similar situation.
www.destructoid.com
Hence why all the Rayman content is from Legends in Smash Wii U and Ultimate.
Nintendo has some level of rights with these franchises. Compare this to say Monster Hunter, Virtua Fighter and the like. They are categorized differently than every other franchise, being at the very end.
Does this mean that Bayonetta was more of a first party choice than a third party one?
Would explain some things.