- Alternative Character Interpretation: The deer. It's hard to tell if the forest is attacking Ponyville and Canterlot autonomously, or if the deer deliberately steered the new growth towards who we know to be innocent civilians. Combine this with Fantastic Racism, and some interpret them as ecoterrorists at best and militaristic warmongers looking for an excuse to invade at worst.
- Anvilicious: The Green Aesop is as heavy-handed as any similar '90s kids film you could name, complete with the Mane Six being inexplicably eager to knock down trees to solve their problems so they can get lectured by the deer and a villain right out of Captain Planet.
- Designated Hero: The deer. King Aspen claims that the reason Ponyville is being torn up by vines from the forest is because a construction company of ponies and minotaurs are tearing down trees to build an amusement park, and they must replant the forest away from the development site to replace the many animal homes being lost; any pony homes destroyed in the process is simply Laser-Guided Karma. He's not in the right, but you can understand his position... until the final panels show the forest's vines have reached Canterlot, and tied up Celestia and Luna and hung them from a tower. At this point he passes Disproportionate Retribution and straight into self-righteous hypocrisy. The blatant Fantastic Racism of the deer and the obvious parallels between them and elves only makes it harder to see them as the heroes.
- Eight Deadly Words: Between the shallow, unlikeable villain, the hypocrisy of the deer squandering what sympathy they had, and the ponies failing to call the latter out or do anything useful on their own, many wrote off "Root of the Problem" by part 1. While the finale had significant criticisms, it failed to cause the backlash some story arcs did, likely because readers had stopped caring one way or another.
- Ensemble Dark Horse: Blackthorn, for being a Reasonable Authority Figure in contrast to Fantastic Racist Aspen and The Load Bramble. Within minutes of taking control of the deer, he invokes Loophole Abuse to ignore the contract that forbids the deer from attacking Well-To-Do, and not only declares full intent to invade the construction site, but recognizes the Mane Six as allies in the task and has them help out by recruiting the forest creatures to fight with them. He's pretty much the only heroic character who isn't racist or incompetent.
- Fanon Discontinuity: In spite of confirming the fanon of deer being the equivalent of elves, the development was disregarded by fan since these deer were everything criticized about the stereotype.
- Hilarious in Hindsight: The portrayal of the deer is remarkably similar to how they were in the highly popular fanfic It's a Dangerous Business, Going Out Your Door. And they were just as unpopular there, too.
- Idiot Plot:
- The story would be over in one page, if it ever happened at all, if any of the characters acted intelligent for just a moment. King Aspen could have sent an envoy to meet with Celestia and Luna in person; Twilight could have used her powers and authority as Princess; the deer and ponies could have taken Well-To-Do hostage when he walked right into Aspen's throne room. Instead the ponies are completely useless to do anything while the deer jump straight to eco-terrorism without any regard for the chaos they cause. Further, the resolution of the conflict (the deer just invade the construction site and kick Well-To-Do and his workers out) could have been done at the start of it all without the need to attack Ponyville.
- Princess Twilight could've simply had Well-to-Do arrested for assaulting royalty after he more than once physically threw her and her friends out of his office.
- Well-To-Do's final plan of action consisted in him kidnapping the king of a sovereign nation and enslaving him to be the mascot of his theme park, apparently assuming nobody would find this an issue. Everyone else seemed to find this a genuine long-term threat.
- Rooting for the Empire: Given all the criticism the deer received many readers wound up rooting for Well-To-Do, if for no other reason then to screw them over. They wonder why the ponies didn't, given the deer proved no better and they would have gotten an Amusement Park out of the deal otherwise.
- Take That, Scrappy!: In the climax, Well-to-Do uses Bramble as leverage to force Aspen to become a humiliating mascot at the amusement park.
- They Wasted a Perfectly Good Plot: This could have been a good arc had it focused on the Everfree Forest or the deer. Instead, we get a straw villain that could make the villains of Captain Planet cringe in embarrassment that still failed to make the deer the good guys in comparison, and a conflict that should have been resolved before the ponies got involved.
- Unintentionally Unsympathetic: What sympathy the deer had for having their forest home demolished, they squandered by invading Ponyville and Canterlot despite their having nothing to do with and being sympathetic to their plight, plus their thinking too little of ponykind to care much.
YMMV / My Little Pony: Friendship is Magic (IDW) Issue 27 to 28