Was Bowser. They actually showed what he was like this time. Most Mario games have Bowser in some random castle built with no apparent purpose with Bowser being like "aw snap" any time he's beaten. He's also too silly in most games. In PM, he was great. First off, Bowser is shown as a threat by the fact that he was able to get all the bosses under his control: Huff N' Puff, Crystal King, Lava Piranha for example. I mean, seriously, these bosses think they're so tough and invincible, yet they all tremor to Bowser. How cool is that? I also love, specifically, Chapter 7 interlude. It's when Bowser is alerted by Kammy Koopa that Mario has finally gotten all the star spirits. He really gets serious this time. It's awesome how secure his castle was. How long it was. How much effort he put into it carefully to keep Mario out. He also tells the Koopatrols to tie Peach up again, but this time for good and if she escapes "heads will roll". It obviously means that he knew that his plan was far too "perfect" that even when Peach got away the last 6 chapters it wasn't a big deal. But now he suddenly realizes even the Crystal King has failed! Still able to remain to sure that he will be able to stop Mario himself even though he beat 7 of the toughtest enemies in the kingdom really gets the player a bit unsure if the final Bowser Battle is going to be a peace of cake how it was in most games.
I don't know where I'm getting at, but when they get into the story of the main enemy as much as they did in this game and so perfectly it really sets off some incredible excitement in my mind as I approached the end of the game.
If anything, Bowser was less threatening than ever to me in PM.
Yeah, he was the main villain, but he was just as silly as he was in the later games. He tries to act like he's tough, but he's still a constant source of comic relief with how often he screws up and with all the jokes made at his expense. Not to mention that this is the game where he admits his love for Peach.
And I actually liked that characterization, personally. Better than the generic evil monster thing he was before.
I agree that Bowser was the most 'hardcore' in the first game, but I found most of your post had to do with the overall buildup of the first Paper Mario. Really, all three Paper Mario had pretty great buildups to their finales.
In Paper Mario, Bowser isn't too clever, but his army of minions and increasing dedication for destroying Mario makes for some fine rising action.
The Thousand-Year Door builds up in several ways. Grodus is also in command of an army, but he's really uptight and full of hatred the whole game. His utter hatred specifically for Mario increases greatly throughout the game, and near the end you realize his unbelievable intentions. For most of the game he appears a genuine threat.
Count Bleck in Super Paper Mario (whether you want to call it a Paper Mario game or not) isn't too sophisticated as a villain. His small group of minions isn't too sophisticated either. But the fact that he overreacted to a simple misunderstanding to the point of attempting to completely erase all worlds with a growing black void is pretty insane.
I like the story progressions for all the games. Hopefully the plotline Paper Mario 3DS will be as effective as in the first three games.