Bowser was portrayed like a complete idiot in Paper Mario, too... In my opinion the only thing wrong with Paper Mario TTYD was the huge amount of backtracking.

As for the topic in general, some of Nintendo's franchises missed the mark last generation, but they were still some of the best games around.

I agree with almost everything you say here. Metroid Prime IS the best selling Metroid game, though the older ones sold better in Japan. I also think that if they release another Zelda game on the OoT formula, it will be quite stale. Bring on either something completely new, or a twist the size of Majora's Mask (woo!). I actually found Twilight Princess to be more innovative in terms of actual gameplay than WW. The puzzles in WW were laughable and almost all the items were from OoT.  The whole Ocean bit and style were neat, but didn't really affect the core gameplay.

Aren't some of the "gimmicky" DK titles supposed to be pretty good, though? Maybe Barrel Blast sucked, but it was from a second, maybe third string development team.

 Bowser has been an idiot in all the Mario RPGs.

I really do think this thread is taking overly critical fans that come with any popular franchise too seriously. The last Zelda, Metroid and Paper Mario were amazing. You can argue Mario Sunshine wasn't as well received as Mario 64 but it was well recieved, no Nintendo franchise has hit the kind of lackluster bumps that franchises like Sonic have.

Not to mention other franchises that weren't commented on like:
Pokemon: selling better then ever
Mario party: not the greatest game or franchises but again selling better then ever.
Super Smash Bros.: always amazing and soon I believe the new one will rock new records for the series.
plus as you mentioned Mario Galaxy is already getting plenty of hype, and New Super Mario Bros. was another huge and loved Mario game.

So I think the whole Nintendo franchises needing to be saved, is quite a bit extreme. the company that needs franchise saving is Sega.

Bowser is the ruler of his own kingdom.  In the original Super Mario Bros. games, he had entire worlds under his control.   In the various games, he typically runs the gamut of a complete idiot and a pretty smart villain that actually has plans.  In the original Paper Mario, his biggest failings were arrogance and being surrounded by incompetent minions.  In Super Mario RPG, it was the same way.  He even saw value in working with his arch-nemesis Mario to save the world.  In TYD, he's just an idiot.  Bad dichotomy there.

As for attacks and what not, I wasn't talking about that at all.  Anywhere.  In reference to characters, I was talking about originality.  Ms. Mowz was original.  Goombella was not.  Vivian was original.  Koops was not.

The story also was weak by comparison.  In the original you had to rescue the stars to gain the power to face Bowser.  In TYD you had to collect star pieces to open a door for a purpose you didn't even know until the very end.  You spend most of the game doing stuff for reasons very hard to justify.

TYD was a great game, but it fell short in certain areas when compared to the first one.

Why is it always about Nintendo? Square has had trouble establishing a second franchise to compliment Final Fantasy. Dragon Quest is not big in the West. Capcom really needs to make new games. They've been living off Megaman and Resident Evil for so long now. Maybe Capcom and Square-Enix can team up and develop a parasite eve RPG, like the first game. Something with a different hook than resident evil.

This list could continue and would include Namco, konami, EA, Ubisoft, Activision and a lot of other developers.

What I am saying is that it is hard to keep a franchise fresh and exciting. Sometimes developers and publishers try new things that may not be a hit with fans. Tomb Raider: The Angel of Darkness is an example of this. But should they stop and keep making the same game? No. They also need to take risk and establish new franchises as well. Or Maybe they could take a page out of EA's book and buy developers.

"We are EA. You are Unique. We will add your uniqueness to our own. Prepare to be assimilated. "

Species 8675: BioWare/Pandemic ---Assimilated
Species 8945: Ubisoft---------------not worth Assimilating

So far i've found the Wii versions of Ninty's franchise's to be better than the GCN version, TP was better on the Wii and was superior to WW in gameplay, Metroid Prime three was the perfect blend of FPS and FPA and more enjoyable than MP 1 and 2, Galaxy is expected to be far better than sunshine, Super Paper mario was different than paper mario, but very fun, its harder to compare them because of the change in gameplay is greater, strikers had online which made it better than the original, Mario Kart and smash on the Wii will have online as well, probably making them better, likely animal crossing Wii will also.

 I do think there need to be more threads about how Square has taken most of their franchises for a ride in the shit factory.

I have to agree ... IMO the best Nintendo games where made in the period of the SNES/N64 ... before that , the now franchises where new games , and had thei own share of flaws , and later came the GC era ... and no comment on that one ( though I liked the GC as a design choice :P ) .

 DK Jungle Beat made by Namco? That's made by Nintendo itself as far as I know.