What a fertile topic! Just a few off the top of my head.
Chrono Cross I think the hype was just too strong on this one; I was bound to be disappointed. It's a pretty good game, just a lousy sequel.
A friend once described it thus: imagine a sequel to
Star Wars that took place on one planet, with an all-new cast. While there are some new characters that vaguely resemble Luke, Han, and Leia, they only appear briefly as ghosts and you find out third-hand that the rebellion was crushed and the Empire won. Actually, come to think of it, that sounds a lot like the prequels
Star Ocean 2 was highly recommended by a lot of people, and I was psyched to try a pure sci-fi RPG. Imagine my horror when the game ditches you in a medieval world 10 minutes in and takes away your gun (the same thing happens in every installment of the series, I later found). The gameplay is all right, but that thwarted expectation stung.
Vagrant Story is another. I remember when all the gaming publications were giving it tremendous scores (Gamespot gave it a 10), without mentioning the ridiculous and unbearable complexity. It's essentially the world's most in-depth mystical weapon forging game.
Like most people, I was awed by the opening cinema and music and lost interest in the first level. While I eventually came back and beat it, the experience only revealed more flaws: distinct dead areas where you have no idea where to go next, and an ultimately incomprehensible story.
I have more, but this is already getting into tl;dr country.
Jam it back in, in the dark.