As many have said Xenoblade Chronicles is leagues apart form other Nintendo games in terms of story, pacing and presentation. But since they acquired Monolith, once the studio was established, I really don't think it is fair to compare it to other nintendo games (to be honest, while I loved Xenoblade, I liked both Baten Kaitos more, and think they should get more love, but since they were made on the gamecube and before Monolith was bought, I don't think they will ever releas a sequel).
On more Nintendo esque games, I loved Paper mario and the thousand year door.
Other games worth mentioning are
Fire Emblem: Path of Radiance
Skyward Sword which had lots of problems, but definitely it's story wasn't one of them
Mario & Luigi games
Primes games, which have excellent atmosphere and lore...but their main story is a little too simple I think