Actually, Nintendo made it kind of possible! Has anyone played Kid Icarus: Uprising for the 3Ds? It made tons of references of Nintendo characters. Maybe just for comical purposes, but it did!
As for pokemon, I dunno. I wouldn't say that in the world of pokemon, they would make direct references to Nintendo characters; maybe small hints of say, instead of Link, just... a boy in green. But, it'd be kind of weird if they started doing that, imo. It'd be an Easter Egg at best, but other than that? Not very likely.