Fire Emblem: Shadow Dragon

Just compared to the other FE stories it's meh.

Xmen Legends II: Rise of Apocalypse. Story was nothing special, but the gameplay was so much fun.

Like every Final Fantasy apparently has a shit story but they're still loved for some reason

I disagree, XIII was not loved. 

I would even mention it here if it was a good rpg (any of the 3).

White Knight Chronicles

- Big World, Big Monsters, a Combat System that can be appreciated BUT it has a very uninspiring story and forgettable/non-charismatic characters.

You'll be missing out on a great JRPG if you won't play S2 because of S1.

I don't think they intended the Neppy universe to have a good story. xD

Fire Emblem Awakening.

Boring/classic story and characters without any charisma (compared to previous games). First time in a FE that I wanted to skip the dialogs.

I never liked The World Ends With You story, even if the gameplay is one of the best on the DS. Maybe it's the characters, I didn't care that much for any of them.

This is another good choice. The wasn't bad, but just kinda there. Enough to keep you moving along, but it's pretty common in Level 5 games.

As for Nep-nep, I actually love the story. The idea of the gameindustri banding together to fight piracy is hilarious to me.

Kingdom Hearts. I wouldn't call the overall story bad or mediocre because it served it's purpose. However the Disney sections were horribly written and reinterpreted to fit into the KH universe.