Have you played the arcade Mario Kart games? They don't feel right. You can just tell instantly by playing them, that they were 100% Namco. They ran on the Triforce arcade board, made by Nintendo, Namco, and Sega, but Nintendo completely licensed the Mario Kart intellectual property to Namco for the game. They did the same thing with Star Fox Assault on the GC (it started as an arcade game on the Trifroce arcade board, but they got too deep and decided it was a full console game instead), and that game sucked too.
If you've played every Mario Kart, you'd disown the arcade ones, and if you played every Star Fox, you'd disown Assault and that Adventures crap. Fuckin' Namco!
(Disclaimer: Namco, I love you, thanks for Pac-Man and Katamari.)
Nintendo and Namco have been in bed with each other since back before they put Link in Soulcalibur 2. But that doesn't mean Link is actually in the Soulcalibur universe and timeline for good now. It was a joke cameo thing for one game. Just like Darth Vader and Yoda in the next game. And Samus and Link aren't in the Mario universe due to their crummy cameos that Square made.
This is all like when Marvel and DC comics make their stupid cross-overs. It's in some parallel universe that doesn't affect anything real, like the fact that Samus ain't belong in no Mario Karts!