Most of Mass Effect 3, for the whole series. The ending, naturally, was crap. Mars just set up the crap, escaping Earth was painful "I'm trying to be cinematic" crap, the Citadel was plot magic crap, as was Thessia... Pretty much everything except Palaven, Tuchanka arc and... God, what was the Quarian homeworld and its arc? Was utter crap. And those 3 were more 'passable' than good, for their own reasons. This of course doesn't count any non-free DLC, as if I put down $100 I expect a full, good game, and extra content purchasable to enhance, ala things like Lair of the Shadow Broker for 2, it. Not a crappy rushed game, and being expected to pay for more content in order to make it passable at best. It just demotivates you for the entire series, when the payoff it tries to build towards, is so terrible in its entirety.
Bioshock... Everything after the would you kindly bit. It turns into a major slow grind/slugfest. Not only is most of your motivation gone, but the game pulls annoying stunts on you and enters the slowest and least interesting slogfest it has, before taking you to a shitty health sponge boss fight. I generally rush through the end game as fast as possible, and just cheese the final fight, because they're that boring.
Dragon Age Inquisition: The Hinterlands. So boring and grindy and yes I want to complete all the sidequests, I'm a completionist masochist - could they have just not made them so boring? The rest of the game was ok, and maybe worth the occasional replay, but dear god that early slog...
Also gotta say everything in Skyrim except a couple of story beats, which are at best ok. Most of it is just utterly uninteresting. I feel like I'm playing the game equivalent of a 3 year old kid's drawing book. Sure, great for me to try and imagine what they've drawn, but I'd rather watch a movie, look at real art, or read a professionally made picture book with good writing, illustration and an engaging narrative.
Exploration missions in SWToR. I mean, ok, you don't have to do them and can skip them, but on my first playthrough of each faction for a given planet, I'll do them just for my completionist self. It just demotivates me from doing each planet when there are so many of them and they have so many parts that are all the bloody same and are so boring. Cannot wait till I'm finally finished Sith-wise so that I can just skip them forever more.
speaking of the ToRs, Taris. Any ToR game, I just hate Taris. I don't know why, but it just annoys the shit out of me. I was almost glad when it got burned in 1, until we had to revisit it in 2, somehow making it even worse.
That awkward pause sort of thing in the middle of Pokemon games where it kind of reigns in the whole gym thing to send you through a few caves that are that bit too long and, especially recently, uninteresting [The older games at least were mazes that you had to learn and explore to get through. These days its just a linear path with puzzles a 2 year old could solve occasionally], to try and further the actual plot of the game, but all it really succeeds in doing is stopping you from getting flight and the other HMs just long enough that it turns into a boring slog, rather than being a cool interlude. Would have been better had they waited until you'd beaten all the gyms, then had something happen - that way you had access to everything, and there's been more buildup, and it is entirely up to you whether you go to the Elite 4 and finish the game on your own merits, or chase down this main story thing that's going on, rather than being awkwardly interrupted from each so that you have to do the other some more.
As for individual bosses, none that I can remember, but I know there have been some that have pissed me off, don't remember what though. Rather than being offensively bad most boss fights are just boring and uninspired, telling you how to defeat the boss, who is just a health sponge to try and represent 'challenge', rather than anything actually difficult, with attack patterns you have to figure out and learn for yourself. Its why I love the Zelda games, and some MMOs - there's usually at least one boss in the game that's a bit tricky to actually figure out, and results in a wipe the first run through whilst you figure out what it can do - an actual challenge, rather than the simple health sponges most games throw at you.