In Super Paper Mario, we were presented with the fact that four of the characters are the main "heroes" in the series. Mario, Luigi, Peach, and Bowser are these heroes. In Paper Mario, Bowser was the final boss. In The Thousand Year Door, a possessed Peach was the final boss. In Super Paper Mario, Dimentio used Luigi's body for the final battle.
I conclude that the final boss in Paper Mario 3DS will be some variation of Mario himself, considering he is the only hero that has not been the climactic battle. How this will work out, I am not sure though.
"Shadow Queen =/= Peach Super Dimentio =/= Luigi" More precisely: - Paper Mario's final boss is Bowser with the Star Rod - Paper Mario 2's final boss is a mix of Peach and the Shadow Queen - SPM's final boss is a mix of Dimentio, the Chaos Heart and Luigi Saying that they ARE the final bosses is just saying it more directly than "They partially are the final bosses because they end up being powered-up / possessed / fused with the game's "true villain" or main artifact etc.".
I personally hope Mario will "be" the final boss. An evil Mario clone created by the main antagonist, or some evil taking over Mario's body and Mario must fight it in his mind, that'd be epic and would make the game worth getting (as if it wasn't worth getting already). --- No Wi-Fi = no online, no WiiWare, no DSiWare. I hate my modem.