I figured I'd mix things up a little. We all list our favourite games from time to time, favourite soundtracks and movies as well. However, what you should do in this thread, is to list some of your favourite games with your least favourite part(s) and feature(s)
Half-Life - GoldSource titles
Island hopping in Xen. Some sections of Xen were great and Blue-Shift showed how Xen could be done really really well. The original title and Opposing Force however, went way overboard with the moving platform / floaty island navigation.
Half-Life - Source titles
Manhacks - Thankfully more rare in the episodes, these are one of the most irritating enemies in any game I've ever played.
Airboat / Buggy sequence - Episode 2 got vehicles right, and a good job too consider a large chunk of that game is spent in the muscle car. The original HL2 however did not fare so well in my eyes. Both the buggy and the airboat sections really irritated me.
Fallout 3
Metro tunnels - I love open world games. The things you can stumble across by chance are a good distraction when it seems as though nothing is really going on. However, the metro tunnels are way too linear and overused to be fun. The first time they can be tricky to navigate and you can still find hidden caches, bits of lore and occasional frantic close quarters combat. However, when you're ducking back into a tunnel to get from point A to point B and you've already cleared it out, it essentially becomes a ten minute loading screen that you can't walk away from. New Vegas did away with these thankfully.
Skyrim
The Main Questline - This one is quite a glaring issue. It's probably only an issue if you were to play Skyrim and for some reason were determined to avoid all side quests or exploration. That is not the best way to experience an open world game at all, especially Skyrim. The main questline is simply really dull. I'd have to do a main story quest, then take a break and explore for a bit, or deal with some of the many, far more interesting side quests.