There are a lot of plot points that bother me, but I'll stick to ones I actively ignore their existence.

Desmond and the First Civilization in Assassin's Creed, I'm fine with a secret war between two secret societies that are battling to control man's fate but I absolutely never cared for the Sci-Fi elements with Desmond nor did I like the First Civilization nonsense. Had I actually cared, I'd probably would have been pissed at AC3's ending but I largely ignore those elements of the plot as much as I can.

The Compilation of VII, I am not a huge fan of VII but even I can't accept how bad these milking titles really messed up the narrative given in VII. So no, I don't believe any of it happened and VII is still a stand alone game. In fact let's just say for the sake of arguments that we'll lump all the sequels to main FF games here as well. So no After Years, X-2, XIII-Trilogy, or Revnant Wings.

I'm starting to think this way about Big Boss's backstory, while I love MGS3, I don't like how Portable OPS, Peace Walker, and MGS4 have painted him as this sympathetic anti-hero whose bulltrout from the Metal Gear titles is handwaved as Snake just not realizing what he was really doing. I like stories about noble figures reaching their breaking point and turning into villains it is just not done as much as I would like but all the post-MGS3 Big Boss stories have basically made him into a good guy who is only evil cause Snake doesn't realize he's working for the bad guys. I prefer Outer Heaven being Big Boss' wrathful revenge against the U.S. government and the world for how it treats soldiers like pawns, not his secret army to wage a secret war with an old army buddy and his A.I. computers. Also I wish they would stop milking The Boss in his stories. Both Portable OPS and Peace Walker have great scenarios that get bogged down with it just being one giant wank fest for Big Boss to moan about what happened to The Boss and reaffirming his belief in what she wanted for him. Peace Walker even has BB forget crap that happened in MGS3. What do you mean you don't know why the Boss did it? She told you like four times in MGS3.