- Anvilicious: The author makes no secret of their rather dim view of religious faiths and their practitioners. Every central protagonist who mentions religion, either in conversation or in their own thoughts, is either dismissive of or hostile towards it. Then just to hammer the point home, any religious characters introduced to the story are either utter zealots and bigots or, if they're not cartoonishly evil, are suddenly and brutally killed off within a chapter of when they're introduced. It's also heavily implied that the reason that humans haven't learned how to utilize their psychic potential by the time of the story is because of religions condemning it as witchcraft and killing its practitioners.
- Base-Breaking Character: Lana has become this. First was the arguing over whether or not her Shipper on Deck "joke" and/or her general antics in the name of "fun" made her hated but, since chapter 20, when her "joke" has come out and she's been given a What Were You Thinking? chewing out, only to explode back, it's gotten worse. Some see her as sympathetic and understandable, others see her invoking a Freudian Excuse as the reason why its Never My Fault.
- Broken Base Some readers were displeased by Twilight's Unstoppable Rage and the subsequent Curb-Stomp Battle she issued in chapter 33, thinking her overpowered and rendering the others worthless. Other readers stepped in with counterarguments and reasons why the feat fell within previously established ballparks.
- Draco in Leather Pants: Discord's characterization fits post-reformation, but is fairly whitewashed considering the story begins pre-reformation. He sent Twilight to Earth to get X-COM and Equus working together against aliens, but although he claims no one would've believed him if he'd told them before, there's no real reason why anyone should believe now instead, nor why he does it now as opposed to the nearly-identical circumstances of his first release. He also poo-pooed friendship in all his canon appearances, yet brings Lana back to life just so she can continue being Twilight's friend.
- Harsher in Hindsight:
- The existence of the Anti-Magic "Equalizers" was bad enough before Season Five introduced Starlight Glimmer and her delusions of Equality.
- Here, EXALT use XCOM gear and uniforms to carry out Terror missions. Come XCOM 2, XCOM itself is using guerrilla tactics against the alien-controlled cities and are denounced as terrorists, accusations that ring even more clear for Commanders that aren't concerned about collateral damage.
- Like You Would Really Do It: An alien monster attacks Spike and the Cutie Mark Crusaders in their Ponyville classroom.
- Rescued from the Scrappy Heap: Vahlen may be on the path to this after the events of chapter 17, with hints of her reasonings for being so antagonistic towards Twilight being confirmed from chapter 15.
- The Scrappy:
- Strawman Has a Point: Word of God states that the council is made up of unknown individuals, not representatives of funding nations. Senator Goleman's political attacks are completely justified as XCOM is a glorified PMC operating as it pleases, not an official multinational force. It has been pointed out that the nature of the Council is not completely known and they may take the form of The Illuminati, which means they not only control XCOM but the nations of the world as well. Strawman still does have a point, but not the one that he started with.
YMMV / Arad's Stardust