Have you checked out marioblaster's Mushroom Madness
thread? He's been working on on a fan film for the movie for something like a year now!
While details are scarce, it appears to be a pseudo-sequel in that it's a continuation of the characters and concepts of the movie, but not of the story. Still, marioblaster has been working on this thing for a very long time. He's actually designed and made the costumes, weapons and items. He's even doing his own SFX, which have been promised to be very high quality for a project of this caliber.
His film is a very ambitious project. There's hope that it will do the movie justice and will begin a series of short films set in the film's universe. While a full-fledged "Super Mario Bros.: The Movie 2" is perhaps outside of all our resources and capabilities, there's no telling what we can do with the right passion.