Final Fantasy 8. Somewhere in here, there's a good story, minus all of the poorly-written romance between an angster and an idiot. Squall's "face" at the end (Look at Faceless Squall in Images and cross your fingers that Rule 34 won't show up) could proabably have an interesting story behind it, other than meaningless symbolism.
It's an interesting story and premise, but it's so caped in shit.
Persona 3, also. They turned a story about normal people having to accept reality and their cessational future into every high school kid in Japan having a convenient tragic backstory. Seriously.
Yukari's got mommy issues and a dead dad.
Ken's mother died because of Shinjiro.
Shinjiro's entire family is dead.
Akihiko's sister died in a fire.
Mitsuru watched BOTH, not one, BUT BOTH of her parents die in front of her.
Junpei's dad is an abusive alcoholic.
Kuromaru's owner is dead, and he feels he has no meaning in his life.
It's all so convenient and set-up, even the fucking dog's got a tragic backstory that the player needs to fix.
Persona 4, also. 1 and 2 had better stories, but probably worse execution gameplay wise. Persona 3+4 still have good stories, but worse execution (somehow). In P4's case, it's the grinding. I'd level the entire party - even characters I don't use in boss battles - up to their neccesary level in order to keep the main character ahead about 5 levels, to cut down on the grinding later on.
And Costume Quest. I love the game's art and humour, but the battle system is directly cloned from Paper Mario. I also love Paper Mario, but I spent $10 on something that wasn't Paper Mario, damnit. Now dance, monkey!