- Ass Pull: Double example: Accord's Order allowing him to control the Elements (when even the narrative itself contradicts such reasoning), and Starlight being able to shield herself from them (a normal Unicorn can somehow do what several Physical Gods couldn't?).
- Broken Base: While most people agree that the third issue is the weakest of the arc, people are divided on its quality beyond that. Some find it flawed, but still a good read and doesn't ruin the arc, with the twist involving Accord and the Elements being dark and surprising. Others find it a poorly written, story-breaking Ass Pull in an issue that completely ruins the entire arc.
- Ending Aversion: Notice how #50 seems to be responsible for nearly all of the backlash?
- Fanon Discontinuity: The final issue's definitely been getting this — what with the sheer Continuity Snarl regarding the Elements of Harmony (thus outright rendering the Rainbow Power a complete "Shaggy Dog" Story), Starlight seemingly having enough Story-Breaker Power to actually invoke Deflector Shield against them (when even Physical Gods like Nightmare Moon, Discord, Lord Tirek at full power, etc., couldn't avoid being Curb-Stomp Battle'd by them), Accord being immune to the Elements because of him being absolute order in direct contradiction of everything said about the Element both in this story and outside it, etc. It doesn't help that the "villain is immune to the Elements for some reason" is an incredibly overdone fanfic plot line.
- Fan Wank: Thanks to the massively unpopular finale, many fans find themselves having to do this. (E.g., "The Elements didn't backfire because they represent absolute order; but because Celestia had tried to fill in for Twilight, Accord had corrupted Twilight beforehand, etc.")
- Harsher in Hindsight:
- Discord switching from Chaos to Order. The episode "Discordant Harmony" eventually made this (sans the Split Personality) canon; only this time, Discord nearly faded from existence as a drawback — yikes!
- Celestia's worrying about being corrupted were already bad enough when she recalled the Reflections arc, but it stings even more now that the main show has acknowledged that she could fall to her dark side.
- Hilarious in Hindsight: Note all criticism regarding how retrieving the Elements of Harmony clashes with the shows continuity and logic, guess what the show did in the season 7 finale? Extra points for the very next comic arc tying heavily into said finale.
- Tainted by the Preview: Right before the first issue of the arc was released, the synopsis for the final installment was released; "When the Elements of Harmony prove ineffective, the final gambit rests in Starlight Glimmers hoofs!" Starlight Glimmer is a hugely divisive character in part due to accusations of shilling her over the Mane Six to make her look better, especially in the Season 6 finale, which has an almost identical premise. The controversy over this has overshadowed nearly any other exceptions for the arc.
- Unpopular Popular Character: Despite making everyone in-story miss Discord, Accord is still regarded as an interesting Blue Oni to Discord's Red Oni, not to mention genuinely Affably Evil despite his creepiness and ruthlessness. Also, his Graceful Loser at the end is likewise a nice — not to mention somber — contrast to the usual Villainous Breakdowns.
YMMV / My Little Pony: Friendship is Magic (IDW) Issue 48 to 50