These are what we call the 'YMMV items.' Things that some people find in this work. We call them 'your mileage might vary' because not everyone sees these things in the same way. This starts discussions in the trope lists, a thing we don't want. Please use the discussion page if you'd like to discuss any of these items.
Broken Base: For What's Done in the Dark..., readers are split over who is less in the wrong: Shining and Luna for literally screwing Cadance over, or Cadance for her tantrum involving maiming her old mentor, trying to have Luna banished to the moon again, and seceding from Equestria.
Complete Monster: For being largely fleshed out through flashback letters, Feather Duster is an utterly horrible piece of work. He unleashes a catastrophic storm over Ponyville after being fired as weather captain (for drunkenly flooding the rabbit warrens during Winter Wrap-Up and orphaning Angel Bunny in the process) just to screw over his replacement Rainbow Dash (orphaning Applejack and her siblings in the process) and would have let Dash face the wrath of Ponyville if he hadn't passed out drunk at the scene of the crime, and when he is exposed, he cares more about being "embarrassed" by everypony else than having killed and apparently decides Dash is at fault for his own situation. Just to hurt her, he attacks the orphanage where she grew up, fatally wounding her mother figure Firefly, and kidnaps foal Scootaloo to make Dash choose between saving her and stopping him from unleashing an even bigger storm. It's enough for Dash to justify pushing him into a Sonic Rainboom point-blank to stop him from hurting anypony else. Then he comes back through the dreamscape to feed off of the fear of the Cutie Mark Crusaders Freddy-style so he can take over Scootaloo's body and murder Dash, before finally being literally bucked into Tartarus and devoured by Satan himself.
Darkness-Induced Audience Apathy: The increasing focus on foreshadowing/setting up a coming cataclysmic conflict which portends doom for Equestria, and the distinct possibility of unhappy endings for most characters involved, has driven off a few readers (though many more are still hooked). Some also find the behavior of the royals who receive much of the focus to be extremely unpleasant, especially considering that their divisive behavior is implied to be at least partially responsible for said conflict.