I have 2 that always bother me:

Character dies..but really didnt story - FF4 and Marvel Comics are notorious for doing this making characters die only to have them survive ni some really stupid outrageous way. In FF4 nearly the whole cast minus Cecil and Rosa and Edge temperally die in some point in the story but all magically live some make sense like Rydia and the Twins Parom and Palom but Cid and Yang!? Cid Suicides bombs a airship how does he survive the bomb explosion tied to ANND the airship? Yang locks him self in a exploding chamber and blows up and both are fine..lame.

In the recent Cival war comic in the Marvel universe super heroes fight each other in a 2 way war lead by Captain America on one side and Ironman on the other, about registering there identities with government some like  some dont. At the conclusion Cap turns himself in afetr he realizes how much damge this hero war is causing and in this during his restrainment he is sniped serveral time leadind o his death which was pretty shocking and aadmiral at the time...but turns out he didnt and the bullet was some magic bullet that trapped his soul in some spactime prison where time freezes...ok

The I was being controlled story - This story usaually happens when a once good guy turns evil...you go through the game egarly awaiting the answer of why is main evil after all hes done being a good guy.. you finally get there beat em and he reveals or the controller reveals that all this time he was being controlled..uggh

Most recent offender is Jin from Tekken 6, this hater of all things evil all of a sudden is evil and has just unleashed a war on the world that is rsponsible for killing millions... but it turns out the main enemy in the game is reponsible for it. though Jin wasnt reallt being mind controlled( h needed to give Azazel a body so that unknown to Azazel he was going to kill Azazel and himself) but still it would of been cool if it was 100% was his own motivation.

overall I hate both these storylines because they feel like a cop out, the first example is the writer having no balls( more at the Captain America death) if your to scared to piss of the fanbase then dont do it, and the second is making a good guy evil without making it necessarily his fault so everybody can magically forget the damge he caused.

So what are bad plots the annoy you?

That character dying thing is actually not just Marvel Comics but pretty much any long-going American comic. It's kind of annoying, because it cheapens death in the comic universe so incredibly. Every time I read Marvel or DC and someone dies I just go "Okay.", because I know they'll be back within a year or two.

I'm usually annoyed by the reasons the main villain has to destroy the world, "I'm powerful so I have to use my power to destroy those who are weak", "I want to be a god", "We are doomed so I'm saving the world by destroying it"

I Hate it when, a toad tells me that princess is in another castle.

In your last point, he wasn't the main villain

None of them annoy me, because I just try to enjoy the game and not over think. But if I had to choose one I guess it could be where the main villain's motive is revealed and it's to *gasp* destroy/rule/take over the world!!

And I don't mean that you could summarize that the villain is trying to take over/destroy the world (there are a lot of villains that have that as a summary, but it doesn't describe them or their motivation/true intentions etc. very well), I mean the villain is just a one-trick pony with no motivation, reason or anything to take over the world other than he/she/it is placed in the game as the villain for all to fight, hate or whatever.

These:

"I want to be a god" - But you're already the strongest person on the planet asshole, that's why I had to level up to 99 before opening the big ass door to your throne room.

"We are doomed so I'm saving the world by destroying it" - Just kill yourself, it's easy. And did you tell your sub-bosses that you were going to be doing this??

That the villians are some cult that want to rule the world. Indigo Prophecy is a very big offender of this.

What game do you mean?

I was thinking of Gilvaroth from Jeanne d'Arc, I think his reason was something like that