The Paper Mario final bosses are as follows: Bowser, then Peach, then Luigi. At this rate it would make sense if the final boss of this game was Mario. The hero becoming the villian in some shape or form is one of the few ways I think Paper Mario 3DS could have a crazier story than Super Paper Mario where all existence was nearly destroyed.
First game had Bowser (the usual evil), second game had evil from space, third game had evil from another dimension, and Paper Mario 3DS will have evil come from below the ground. Meaning Mario will take on the Monty Mole Empire.
http://epicvideogamers.com/ I've been waiting for Nintendo to reveal a handheld with the 3DS's graphics since 2003.