A lot of the story took place outside of the game via books and comics. They're pretty good actually. Maybe not as much if you don't like Halo, though.
But basically, the main thing that turned me off was that in Halo 4, Cortana sacrificed herself for Master Chief, the good of humanity, etc. And then in Halo 5 she came back as the villain. It was just...not cool. And wasted the meaning of what she did in 4.
Code Geass, Death Note, Gundam (Seed I think), freaking Star Wars- all have had extremely likeable characters go to the dark side.
An effective villain creates emotion that even the hero can't (outside of dying and that rarely happens outside of a martyr scenario at the very end of the book, film, etc). That emotion sells the conflict, investing you in the story. Betrayal is a powerful mechanic in creating emotion and to many people is more relatable than say the acts of a homicidal maniac. I've never been affected by a murder or a holocaust but I have had a significant other go from best friend / biggest part of my life status to sleeping with some rando she just met, not only completely ending the relationship but completely rearranging my life's direction. The thought of her evokes much more emotion than even my ex-fiancé who chose drugs over the two children we had together.
Needless to say I hate a good guy I like goes bad but it generates so much emotion that I'm into that story, I consume it.