I've heard this business about Yoshi being grouped with the Mario characters. He started as a Mario franchise character and always will be as far as I'm concerned. He's always been marketed that way and grouped with them in Mario Party. Donkey Kong has only recently branched away again with the successful revitalization of the DKC franchise.
Shulk appears with the 3P characters because his game was created by a studio with a long track record of publishing for other consoles. Xenoblade was 1p published, but made by what is still essentially a 3P dev.
All of it makes so much sense. The only two remotely strange things here are: Game and Watch: why is he by Mario? Then again, there was this:
So Sakurai could be lumping him into the Mario row for that reason.
The other strange thing (but not really) is Little Mac away from the classic NES characters, but that's easily explained because his franchise has had iterations on SNES and Wii, so maybe he's not considered enough of a throwback.
Everything else fits like a Power Glove.