The Elder Scrolls IV: Oblivion, Final Fantasy XIII, Fallout 3, and Breath of Fire: Dragon Quarter.
Oblivion felt like I was being rushed as fast as possible to the finish line, and that made me lose interest, especially since Morrowind had you explore and make friends before being allowed to get the next main quest.
FF13, well I'm used to FF games being more-or-less free-roaming and having interesting NPC interactions, but since it was just straight lines even less complex than Mario Bros. 1, and no NPC interaction, well if it wasn't a FF game I wouldn't have bought it.
Fallout 3! First time I played it, I didn't like it because I thought the game was free-roaming like other stuff Bethesda does that scales monster spawn to your level, but the first thing I saw was the ants. A year later I played it entirely on god mode just to see the story, and out of fear of the ants. So what if I'm lame? Then I beat the game (easily without god mode, pretty much beats itself) and didn't get to continue playing after the end of the story. I wanted to see the clean water, and I wanted to greenify everything, or at least finish some quests. Stopped the story dead in its tracks, as well as my interest.
Breath of Fire: Dragon Quarter I hated. I don't remember what I liked, sorry, it's been too long. I do remember that being a dragon too many times gave you a game over, no matter what you did. In none of the other games did it do that. Plus the enemies were strong enough that if you weren't a dragon, you wouldn't survive most the random encounters. Force you to game over before you're anywhere near the end? I stopped playing once I realized that.