MGS2

It didn't even really happen...that's pretty weak Konami.

Animal Crossing all they give you is that your being drooped off in this town don't screw it up...

That

Or Mario for not changing the story after so many years

Ill have to agree with Mario. The story for Mario Galaxy was so generic. Its like why even bother with a story. Just save the princess. And if you are going to have a story like that at least have some voice acting instead of mostly annoying catch phrases.

For an RPG, Sword of Mana had a pretty bland story. Enjoyed the game though.

Alternately to my post above
Sonic Chronicles's plot was fail, and (Spoilers I guess) OMGCLIFFHANGER

First of all, Final Fantasy X was a masterpiece in nearly every way
Secondly, I also liked God of War, I do like the mythology and locations, even though you may not call that story, rather time period and setting
Thirdly, are we looking for games that have no story, or those that just have an excuse of a story or games that try to have a story and fail miserably?

Because for the first one, something like BP has to win, then for the second one, it would have to be mario, then for the third one, Ace Combat

Ace Combat 6's story was so awful that I began skipping the cut-scenes after a couple. They were so dull, nonsensical and poorly written

Agreed.

On-topic: Mario Party series have the worst storylines.

Out of JRPG's it would probably be Magna Carta, an absolutely awful JRPG.

Out of all games, probably Mario Party.