There's quite a few of these, and I hate to admit it a lot of the time. One big one recently was Skyward Sword, it's not that I didn't enjoy it per-se, I just didn't love it as much as other games in the Zelda series. For me, I enjoyed the LoZ games which added a sense of exploration and discovery such as Ocarina of Time, Twilight Princess, and Wind Waker. Each of those games allowed you to freely roam a larger expanse of areas. Within Skyward Sword, you're pretty much limited to the sky, which incidentally, does not actually have a whole lot to see and do. It did bother me that the entire game only really had one town to visit, which hampered the diversity for me. Amazing gameplay and dungeons, as well as story-telling, but thanks to the lack of exploration, the replay factor died a bit for me, and it rendered the post-game redundant as there was pretty much nothing to do.
World of Warcraft, and almost any MMO, bother me. While I love Western RPG's, and RPG's in general, I find MMO's to just really lack storyline and consistency. Quest systems have so much potential, but I've found these games to lack drive and strong design. The same goes for any top-down MMO's, I simply cannot stand games such as League of Legends and Diablo 3.
Mass Effect is another game I struggle to get to terms with, while the series has some of the highest rated games of all time, I have yet to enjoy it much. I find the setting to be overly sci-fi and I suppose that's not a genre that interests me too highly. In saying that, I did pick up the first Mass Effect for 99c, so I might give it another go. I do love my RPG's as I've said before, and while Mass Effect is intended to be one of the finest in existence, I'm struggling to relate to it.
A big one is Dishonored. People have been giving this game massive praise, but I found it to be really badly polished. The start of the game did nothing to engage me, and I feel that if a game can't get you to be engaged within the first hour, it's already failed on you. I know a lot of people enjoy this game, and it does have a lot of positive points about it, I felt it did lack the strength to grab me in and make me want to keep pushing. I never made it to my second hour.
Assassins Creed 3. I love this series, it has some extremely strong points, and I would consider myself very faithful to it. However, the only thing I really enjoyed about this game was the online multiplayer. While it did look great, I found it to be a really buggy and unfinished game, which again, lacked a lot of finesse. It's one I'm almost finished, but find myself struggling to do so. I feel that Ubisoft are certainly cashing in big time, even with AC4, they knew that the most fun thing about AC3 were the ships, so they're making a game where you're a pirate. I'm beginning to lose faith in Ubisoft, so I hope they take more time to polish this one, which is doubtful given the release date.
There's quite a few, and I know my opinions would easily come under fire for them. But alas, we all have our guilty hates.