Well I mean we already got the Smash Bros. series which in a sense introduced the Pokémon world with all the different franchises Nintendo owns. Now, I know that obviously Smash isn't an actual Pokémon game but consider it for an instance. Final Fantasy I made a reference to Link in a gravestone, without giving to much explanation about it, and nothing really happened. I believe that small references just like that could enchance the game experience of any player... maybe, I don't know... As long as they don't make Bowser a Pokémon... Imagine in the next Smash Bros. game playing as Poke-Bowser...
That would be weird...