Bowser's Inside Story might end up being my new favorite Mario RPG when everything's said and done, and it's strictly because Bowser is so freaking awesome in it. The Mario & Luigi segments aren't anything special so far (they feel sort of recycled from past games), I'm not feeling the new characters (especially those weird-ass Globin things)... but everything involving Bowser is gaming at its absolute best.
Just imagine how awesome a game solely starring Bowser would be. That might even be better than "Paper Luigi"!
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"Claire likes to say 'You can be part of the problem, or part of the solution.' But I happen to believe you can be both." - Phil Dunphy
The thing that makes Bowser's Inside Story so amazing is that they don't sacrifice the "Evil King Bowser" part of his character. Having him randomly become good would have ruined the whole package.
Unfortunately, I doubt that Nintendo would sanction another Bowser-focused game without including Mario as some sort of moral compass/anchor. Hopefully I'm wrong!
Most Mario characters become 10x more awesome in the RPG games. Even Peach is pretty good in the Paper Mario games. Bowser is probably the one to receive the biggest "boost" from the RPG games, though (Paper Mario and BIS Bowser are amazing).