Eh, Bethesda games are interesting.  They have some lackluster stories mixed in with some pretty good stories.  Overall I consider the story of fallout 3 to be good, certainly isn't bad or mediocre.  Not great, but good.  Same can be said for just about every elder scrolls game.

This is my first post on this forum despite being a lurker for two years. Anyway, these are my choices from the RPGs I've played through:

1. Dark Cloud 1 and 2: They had great gameplay mechanics and I love these games to death, but the story is pretty forgettable.
2. Final Fantasy VIII: I love this game more than most of its detractors, but the story is pretty incomprehensible and contrived.
3. Pokémon: I don't think this needs explanation.
4. Star Ocean 3: Amazing sense of adventure and great gameplay, but the story left something to be desired.
5. Xenosaga I and III: I admit, I couldn't play through Xenosaga II because it was so unbearably bad. In any case, Xenosaga I and III had good battle systems and excellent minigames, but even as someone who has read Nietzsche extensively, the stories are incomprehensible. The games also lack the sense of humor and strong characters that made the story for Xenogears enjoyable in spite of its similar inability to make any sense whatsoever. I admit, I have never played through Xenoblade Chronicles, so I can't offer any judgment on that game.

I will note that I didn't include games that had mediocre stories if they managed to have engaging characters. Games like Fire Emblem: Awakening can compensate for its lack of strong central narrative with interesting and well-written character development.

Really? Because both F3 and Oblivion have very run-of-the-mill stories in them. I'm talking, obviously, about the main story, not other small setpieces you can find in secondary missions (which is what I kinda think the OP is asking).

risen 1-3

Final Fantasy X.

you being a figment of anothers imagination, and that dream inside a dream stuff..... I know the japanese love that stuff but... meh.

Dont get me wrong, I really enjoyed FFX, but not really for the story.
I loved the music, the gameplay, the scenary, the characters and their interactions.... the underlaying story itself? not the greatest thing ever.

Mod edit - added spoiler tag

This isnt only true for RPGs though.... holy cow there are alot of poorly written story lines for all types of games out there.

Well, relative to other RPGs I would still rate their main stories as good or ok.  

I know, but RPG's typically have good stories and some are praised soley for that. You don't really expect a good story out of a platformer or a shooter most of the time

Dude, ffx is still getting rereleases and there are bound to be people on here that haven't played or finished the game.  You need to spoiler tag that!

Whatever, you would have to be willing to buy a playstation in order for that to be true.