Darkness-Induced Audience Apathy: Both of the sequels are heading in this direction. While the original story was fairly dark, it still ended up being a case of Earn Your Happy Ending, avoiding this trope... until the sequels, which pulled some downright brutalHappy Ending Override, especially where Rarity is concerned, which turned off many readers. To put it in perspective, both sequels have the Tragedy tag, which is basically just an advance warning that a story cannot possibly end happily.
Evil Is Sexy: Rarity's birthday gift to Twilight was teaching her how to highlight her natural good looks. Then she turns evil, and really gets into keeping up her looks.
Sweetie Belle, post FaceHeel Turn, also qualifies. She comments on how she's just as beautiful as Rarity, and starts flaunting her looks even more than Queen Twilight does.
Harsher in Hindsight: Inner Demons II shows that Diamond Tiara's bad attitude was because of her mother. "Crusaders of the Lost Mark" would make that same reveal.
Jerkass Woobie: Twilight Sparkle pre-FaceHeel Turn. The Bad Dreams telling her that her friends, family and mentor still hates her for trying to do the right thing wasn't a particularly happy memory for her.
Les Yay: As is popular in fanon, Rainbow Dash and Pinkie Pie's subtextual Les Yay is upped to them having crushes on each other.
Moral Event Horizon: Queen Twilight crosses it big time with her "coming out party". First there's the Sadistic Choice listed on the main page, which is quickly followed by locking Applejack, Fluttershy, Rainbow Dash, and Pinkie Pie in Sugarcube Corner and setting the building on fire in an attempt to kill them.
Trixie finally crosses it when she nearly kills Rarity during the Battle of Fillydelphia. What makes it worse is that at the time, Rarity was shielding Apple Bloom and Sweetie Belle from a collapsing building and had no chance at protecting herself.
In the sequel, the Sons of Midnight cross this when they sacrifice every living thing still in Ponyville, and some of the Everfree just to loosen the seals on Tartarus.
Twilight considers Rarity having to die and be replaced by Vale one of these, since Vale is nothing like her friend.
No Yay: Twilight Sparkle and Shining Armor gets more shippy after Twilight succumbs to her darkness.