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.
Debatable, you could see it coming a mile away, and after all, if the Cult of Nightmare Moon could put the power IN to Nyx, it's fairly obvious that Luna could take it back OUT.
Author's Saving Throw: Arguably the intent behind the retcons on August 5th and 29th, or at least the attempt to respond to what the authors felt were justified concerns.
Base Breaker/Idiot Ball/OOC: Some believe Celestia's actions are extremely stupid or out of character. Others believe she might be acting out of emotions rather than logic or seeing Nyx as too big of a threat to do anything else. It should be noted that as of this post, the story isn't complete, so there is still time for an explanation to be given later.
If what Nightmare Moon claims is true, Luna running away from her, crying for Celestia to come save her might be considered similarly. Also, Luna's What the Hell, Hero? involves Luna yelling at Celestia to stop treating her as a child, among other things.
Of course, given the vaguery concerning her official personality, it's very hard to make an argument that any interpretation of Luna is behaving out of character. This is further compounded by the above scene being the one that establishes Luna's character within Past Sins.
The authors have since changed Celestia's characterization to better reflect that of the show, so this trope might not apply anymore.
Nyx herself is seen as adorable by some, and a whiny Mary Sue by others.
Ironic, since apparently every single revision was done precisely to counter that complaint.
Broken Base: The instant the authors gave in to the protests of several commentors, the opinions of several readers on the story were pretty much completely inverted. Some who prefer the old version feel the revision has ruined the whole story, while those who asked for them are now claiming the story deserves its 6 stars.
On the plus side, at least the authors themselves are happy with the changes.
To clarify, much of the hype came from overly excited fans who over-hyped the fic, which lead to the backlash. It's mostly well-received on Equestria Daily and DA, while places like /co/, /pony/, and Ponibooru despises it.
Moe: Nyx could give Fluttershy a run for her money.
Moral Event Horizon: After the Retcon, Diamond Tiara and Silver Spoon's making Nyx cry and reveling in doing so may qualify. Also, given that they clearly know that the Everfree Forest is filled with monsters, their sending Nyx into the heart of it as a "prank" knowing that she could be killed is unforgivable.
Granted, with all the times the Mane 6 and the Cutie Mark Crusaders have wandered in and out of Everfree, the menace of the woods MIGHT have been a little undermined.
Nyx herself thinks she crossed it when she didn't realize Twilight received a blessing from Nexus and was almost hanged, Nexus may have crossed it for trying to kill Twilight and make Nightmare Moon evil again.
They Changed It, Now It Sucks: Even though the authors and the pre-readers are happy with the changes, some readers got upset and literally said that the changes ruined the story.
No one, and I mean NO ONE, expected the Luna we got…Brian Blessed in a pony suit.
They Wasted a Perfectly Good Plot/Character: Considering the fact that the plot dwells around Nightmare Moon being resurrected as a being separate from Luna, some readers were disappointed that Luna played such little role in the overall story.
Nightmare Moon herself, a major complaint is how Nyx barely acts like her past self and find the ideal of Nightmare Moon slowly becoming good would make a better story.
Wangst: Nightmare Nyx has a tendency to do this in later chapters It's probably due to this that this fic gets its Hatedom from. That and the fact that the Paper Thin Disguise before chapter 10 works a little too well.
YMMV, of course, but the authors did one last revision in preparation for the final three chapters and tried to tone it down. Say what you will about Pen Stroke and Batty Gloom but they listen to their critics.
The Woobie: Nyx. Whenever she feels sad, you can't help but want to give her a hug and tell her that everything is going to be alright.