There are two I can think of:
Fallout 3: It was one of my first PS3 games specifically because I'm a huge fan of the original Fallout (and Fallout 2 is alright I guess). I enjoyed it quite a bit back in the day though it never came close to the original's greatness. Nowadays I can't really play it and have as much fun as I did before. The story is very poorly written, the ending is a mess and the gameplay feels very dry when compared to the much superior New Vegas. Every time I think of playing F3 again, I remember I have New Vegas and play that instead.
GTA San Andreas: As with most teens who grew up playing this game, it used to be my drug. I must have beat it at least 3 times back in the day. Replaying the GTA series in recent years, It's simply not as fun. While the open world and the amount of stuff you can do is nice, the story and characters are pretty bad. Granted, GTA has never been a series known for its stellar writing but I was much more engaged with GTA IV's story since it had believable characters. Going back to SA and its poorly written unlikable characters kinda sucks. Some of the missions are really annoying like the one where you have to pass all the tests in the airfield, the controls for the planes just suck too.
It's not a bad game but I can't go back to it with the same enthusiasm I had before. I beat GTA 3, VC and SA a year ago and I ended up liking VC much more than I did as a kid. The story isn't great either but the characters are much more fun and it has less annoying missions. Not to mention the awesome soundtrack!