Well it's not all Nintendo... if Nintendo had something to say about it, why wouldn't EIDOS/Core, Ubisoft, Namco etc?
Nintendo might actually be glad. Atari or whoever developed must have respect for these franchises for them to have found their way into the game. Putting Nintendo on the mind of Ps2 owners is no bad thing. Gamers will appreciate the joke/homage.
It's an awesome idea... games tend to pay homage to movies and books all the time.... games paying homage to other games? It's a great thing to see even if it's going to take the piss / be tongue in cheek about it all.