Sticker Star! It has a bunch of charm to it, but it really lacks a character-driven plot.

The battle system and gameplay were unique and enjoyable, as well as character animations - don't get me started on the top-notch soundtrack.

Level designs were the best of any Paper Mario. It just lacks character progression (greatest character progression was Wiggler).

Most Pokemon and Tales of games

Pokemon games, by a country mile. Literally, the stories offer little deviation from the norm. How great would a more mature pokemon game would be.

Many JRPGs in general, they are stuck in their way. You can only save the world with teenagers so many times.

SMT IV.

Duh, and Pokemon. 

Every single RPG I played had a mediocre story. Because when it comes down to it they are all about the same thing. It's the characters in it that spice up the story.

Pick a random action RPG (you know, something like Diablo). The chances are its story isn't great.

Kingdoms of Amalur Reckoning.

Most Pokemon games except Explorers of Sky and arguably B/W and the sequels. Another one would be... let see, I'm thinking as I type this out... oh god... you guys get to hear my thoughts... umm... damn. I cant think of any. Well, I'm sure after I read the comments after I post this I'll be reminded and feel like an idiot for not remembering them v.v XD

Muramasa as a ARPG was a huge disappointment to me after Odin Sphere.

Also Neptunia series moeshit is pretty hardcore as far as mediocrity goes, though some sequence are indeed funny if your neocortex falls asleep after a few hours of play.

Paper Mario's story may be simple but that doesn't make it bad, I think a simple story is better than a convoluted non-sense like some games have (cough*FFXIII-2, KH 3D*cough)