I think it would be cool to have a new game where you could be everyone in the Mushroom Kingdom (but mainly Mario) fighting off a new force. It would be like, Bowser is forced to join forces with Mario just this once so that this new force doesn't take over.
It would be cool if they brought over the X-Nauts from Paper Mario, and have THEM be the threatening force (with a new leader obviously since Sir Grodus was killed in PM2). But I doubt they'll do anything like that. I have a feeling the things in the Paper Mario world won't cross over into the 3-D Mario world.
If Toad is a mushroom and a mushroom is a fungus, can we say that Toad is a fungus?