Bioshock comes readily to mind. The gameplay was meh, the atmosphere passable at best, and the story. if one were generous enough to call it that, was predictable down to the beat. Heck, even the sequel was more engaging.
Other than that, Fallout 2. It's a perfect example of a perfunctory sequel - the story was recycled from the original {we're kicking you out to find the plot macguffin, oh there's a bigger threat that threatens everyone} and the NPC dialogue was a constant game of Guess The Pop Culture Reference. A perfect example might be the boxing agent's monologue in New Reno which I thought was actually a clever bit of self-deprecative metahumor... which turned out to be lifted neatly verbatim from an episode of X-Files. The wider world, minor gameplay improvements and companion NPC personalities were high points, but not nearly bright enough to carry the rest of the game.