I'm just going to go on recent memory rather than dig through all the games I've ever played. In that case, it's probably Assassin's Creed 2. I know a lot of people say this is the best and that the franchise just went downhill after this one, but this game just really got on my nerves to the point where I completely stopped playing the series. The thing is, I loved some of the additions to the game, such as the ability to lower your notoriety, or the Assassin's Tombs and Templar Lairs. There was also more incentive go go around the levels, and I enjoyed building up that one city. The thing is, it was so boring and repetitive. Once you free run across one set of rooftops you had virtually free run across them all. The combat never evolved past "hold block, wait for enemy to attack, decide to counter or dodge, counter or dodge, attack". On top of that, stealth was either broken or it destroyed any suspension of disbelief, which was only made worse when stealth was mandatory. The free running controls were still not designed well for any rapid changes in direction or precision jumping, but they still felt the need to force it at times. Oh yeah, and the game was really easy, to the point where the only challenge was in fiddling with broken mechanics. What's worse is it lasted for 30-40 hours if you wanted to do the few interesting things, and they didn't even have the courtesy to at least make you feel like an assassin, which was the major strength of the first game. You just felt like any other protagonist from any other game who was only an assassin because he was part of a group called The Assassins. And then it all ends with arguably the worst final boss I've ever played. Seriously, all I had to do was equip the shortblade and just spam attack him with it, and the fistfight only lasted as long as it did because they needed to get through the whole conversation (the guy was on one life for about half the fight!).
Toping off the annoying gameplay was the story. I don't mind if a person wants to talk about religion in a story, and I also don't mind if they let their biases come through in the story. Xenoblade Chronicles did it, and I love that game. Even the first game managed to pull it off the discussion well. However, Assassin's Creed 2 felt more like the writers were just preaching to us, trying to force their ideas down our throats. There was no room for actually thinking through the issues, just seeing things how they wanted you to see it, and not even trying to be subtle about it. Even when I was agreeing with them I couldn't enjoy myself. If I wanted that kind of obnoxiously dogmatic attitude, I'd just go to my local Christian bookstore and pick a random fiction book off the shelf. What's worse is that that random book, though openly biased, might be less dogmatic than this game was.
Needless to say, I can't think of many games that left such a rotten taste in my mouth that I not only have as little good to say about it as this one, but I also am repulsed at the very idea of continuing to play games in its franchise. Even my love of pirates is having trouble overcoming my dislike of the franchise when I consider getting Black Flag.
However, if I really go back, my least favorite game that I completed might be The Incredibles: Rise of the Underminer. I don't remember much, but I do remember a short, boring game that had one of the most broken co-ops I've ever played.