Due to an extremely repetitive storyline, I am not going to say pokemon, but some games I found that had amusing storylines (maybe not "excellent", but its worth a look into) are:
My World, My Way (Pretty generic story, but amusing in a cute way)
Atelier Annie (Similar to the above)
Nostalgia (Great RPG, though I never liked the coverart xD)
Kingdom Hearts (Decent IMO though it didn't have as much story backing as I would have liked)
Lux-Pain (Peculiar, but intriguing)
Shin Megami Tensei (Haven't really played, but from what I have played, its as good as any visual novel and then some)
Take the eggs! Ornithorhynchus Anatinus GO GO GO! (So its not a commercial game, it still has a funny storyline)
FFCC RoF (Both FFCC are too short for my liking, but both have great generic stories)
FFCC EoT
Another Code (I loved this game xD. Anime style + puzzle kept me addicted and playing nonstop until I beat the game. Its a little short though)
Time Hollow (Same description as Another Code)
Megaman Zero series (maybe not as epic as the Megaman X series, but its still meh)
Rhapsody - A Musical Adventure (Regular grinding RPG with a typical Shoujo story, it's surprisingly not that bad)
Rondo of Swords (Decent Tactical game)
Phoenix Wright Series (I'm sure this is a given)
Luminous Arc Series (I liked the first one a lot, the second one I don't understand as well)
Professor Layton Series
theresia...-Dear Emile- (the fear factor is dulled by the fact that nothing actually attacks you)
Avalon Code (Amusing system and a good story)
Chronos Trigger (Classic awesomeness)
Suikoden Tierkreis (Its great after taking out their stupid english voices xD)
Retro Game Challenge (ok, not that amazing of an story, but its fairly fun)
TWEWY
World Destruction