I had a similar experience with movies. Watching movies was my favorite hobby, then it was entirely ruined when I watched the second Hobbit movie. I found it so bad that it ruined everything that I watched for a year. I constantly picked holes in the plot, relationships, acting, everything.
Ironically enough it was the third Hobbit movie that fixed this obsession for me. That was because it was so close to being good, despite still being an awful movie. I realized why it caused this change in me to happen, so hopefully this will help you with your situation.
Make up your own story. And by this I mean pretend the issues aren't there. Every piece of art is flawed, even masterpieces, which most people are willing to look past due to the fact that the rest of the piece is exceptional. But for others who create the art, it is easy to spot what could have been done differently.
So imagine that it is different. Iron out the creases in your own mind. Rather than not trying to analyze the work, go into too much analysis. Think past what is on the page and make up your own ideas about what could have happened behind the scenes to make it make more sense.
If you disagree with the motivation for a betrayal, conjure up your own elaborate backstory that explores a deeper motivation for the character that explains in your own mind. If a character literally defies the laws of physics to overcome an obstacle (looking at you 'Legolas running on falling bricks' scene), just pretend it didn't happen, and something else happened entirely.
As an example, I love the Darth Jar Jar theory of Star Wars: The Phantom Menace. A movie that I previously didn't particularly like is now actually incredibly entertaining by over-analyzing things that happen in the film, and coming up with a unique theory as to what is going on behind the scenes.
It will allow you to more easily distinguish how good pieces of writing are. There are great pieces of fiction with boring parts, and there are utter train-wrecks with incredibly engaging individual scenes. You can discern the good from the bad, and it's actually a really good thing.
There are some things that are so bad that they are unsalvageable, and so good you will be immersed and never need to do any over-analysis to fix them in your own mind. Either way, you can appreciate them for what they are. Then you can start to appreciate the flaws, and understand that nothing will ever be perfect, but still like them anyway.