Whoa, lots of people listing FFIV in here. I personally loved it, it became my #1 FF game and one of my favorite RPGs ever. I can't say I wasn't disappointed at first, given that it could be SO much more as a remake, but in time I learned to forget about it and enjoyed it for what it was. Liked it better than the original is almost every single aspect.
My personal letdown was Summon Night: Twin Age. I waited anxiously for the game, but the final product was so different and in most aspects, inferior to what I envisioned I just couldn't stand it. Never went past the 1st battle.
Another letdown was Harvest Moon Island of Happiness, the touch controls killed the experience. More recently, Big Bang Mini as well.