Alternate Character Interpretation: Lyra and Bon Bon got engaged in the previous episode, but are shown separated in this two-parter, sticking with their respective races. By contrast, Unicorn Sugar Belle sticks with her new husband Big Mac among the Earth Ponies. Did Lyra and Bon Bon buy into the rumors that badly, or did each of them figure the other was safer sticking with their own kind than being harassed by the other's race and insist on it? If it's the latter, the reason Big Mac didn't insist that of Sugar Belle could be because he knows he could easily take on anyone that tried to give his new wife grief. It would also explain why we see the tightly-knit CMC separated.
Anti-Climax Boss: The Windigoes. While making Equestria colder, they didn't get to actually freeze anything onscreen before getting blasted away with rainbow lasers, and Chrysalis's plan to use them for Engineered Heroics doesn't go anywhere.
Angst? What Angst?: The fact that much of Canterlot Castle was destroyed is barely acknowledged by anyone. The most we get is Twilight casually saying that they'll have to re-build, before heading off for a celebration snack. Though considering Discord can just snap his fingers and fix everything instantly, it's not that much of a concern. Plus you know the old saying: a kingdom is its people, not its castle.
Whether the villains should have been offered a Last-Second Chance rather than being turned to stone on the spot. Some feel this would have fit better with the series' message, and that it could have been handled well, as their character development over the season (such as briefly considering reforming in "Frenemies") would have made this a rare case where a villain redemption had been set up well. Others feel that the villains had made it clear that they will never consider friendship or reform, and that they were willingly evil of their own accord after betraying Discord.
Discord being forgiven for his role in events, and being the one to decide the villains' fate (and to perform it himself). Some feel this was a fitting way to make up for his actions seeing it as him using his powers for good to put a stop to evil, fixing the mistake he made by getting rid of the threat, while others feel that he had no right to punish them when he was responsible for all their crimes. There's also the fact that Tirek and Cozy Glow were already serving their sentences, and wouldn't have been in this position at all if he hadn't broken them out.
While most would agree that Chrysalis and Tirek deserved to be turned to stone as punishment for their crimes, there's the matter on whether Cozy Glow deserved this fate due to her being a child. Those for it argue that she's been such an irredeemable monster who was quite aware that she was attempting murder and seeing her getting her comeuppance instead of being Easily Forgiven like other previous villains comes across as fresh and cathartic. Those against it feel it comes across as unnecessarily cold, since no one tried getting through to her.
After seeing the trio destroy the royal Canterlot Castle, actively sow seeds of distrust in all of the ponies, unleash the Wendigos, and threaten to rip off Spike's wings (all combined with their past actions as villains along with it), seeing the Princesses and Discord turn the remaining villains into stone is quite satisfying. Plus Discord finally got to pay Tirek back in full for manipulating and betraying himnote And Chrysalis for ponynapping Fluttershy.
On the flipside, it's very satisfying for the Princesses to cast aside their Worf Effect status for once and use their powers to the fullest. As full as they can without magic anyway. While they do get defeated offscreen anyway, it's nice to see them go down swinging for a change.
Fanfic Fuel: During her time in the Crystal Empire, Twilight remarks that if something goes wrong, Flurry Heart would be the last hope for Equestria. The ideas for a What If? story are ripe for the plucking.
Harsher in Hindsight: The pony races finally mending their bond at the end of the episode is heartwarming...only for the events of My Little Pony: A New Generation to completely render all that meaningless with all of the pony races showing Fantastic Racism towards each other once again, albeit hundreds (or possibly thousands) of years down the line.
Heartwarming in Hindsight: Twilight's speech about "others who will continue our mission after we are gone." becomes this in My Little Pony: A New Generation where hundreds (or possibly thousands) of years in the future we meet Sunny Starscout who along with her new friends do just that, in spite of the Fantastic Racism plaguing Equestria at the time.
Karmic Overkill: Chrysalis, Tirek, and Cozy Glow were supposed to have proven themselves so Beyond Redemption they deserved their Fate Worse than Death of being permanently turned to stone by the heroes. But their actions weren't seen as any worse than their prior crimes or what Discord as Grogar was forcing them to do anyway, and Discord never made any effort to redeem the trio despite the fact that, unlike the uncontroversially killed off King Sombra, they had shown themselves to be capable of friendship to some extent and had numerous Pet the Dog moments. This caused many fans to think their punishment was unfair as they were forced into a position where it seems they would have been similarly punished even if they hadn't proven to be so irredeemably evil. Cozy Glow got this extra hard as she was already seen as this over her prior punishment, as many believed a child didn't deserve to be thrown in Tartarus when adult villains with comparable crimes were given greater leniency by the heroes, and she had committed fewer major crimes than Tirek and Chrysalis, yet was identically punished.
One-Scene Wonder: Much like with Cozy Glow from the previous episode, Pinkie Pie with Discord’s chaos magic is one of the most memorable scenes in the episode. The fact that she can actually use the chaos magic makes it all the more hilarious and/or terrifying.
She Really Can Act: Not that anybody ever questioned her acting capabilities to begin with, but Tara Strong really sells her emotional breakdown as Twilight when she laments to her friends that she can't find a solution to stop the villains, with many citing this as one of her best performances within the show.
Being among the last fighting-fit side characters, Princess Cadance and Shining Armor were ready to help... only for them to be benched again due to their infant daughter and the Crystal Empire being Twilight's contingency plan. They didn't even participate in the Final Battle! Not to mention, both of them still had big issues with Chrysalis that wound up getting solved by Starlight in their stead.
The Cutie Mark Crusaders don't play any role in the finale, despite their personal connection to Cozy Glow. While they might not have been able to fight, it would have been nice for them to have some interaction with her.
The idea of there being an Enemy Mine between the Legion of Doom and the heroes, whether it be against the real Grogar or the Windigoes, is a very interesting concept that never comes into fruition.
Having all the characters who got worfed over the 2-parter be part of The Cavalry due to a downplayed form of Climactic Battle Resurrection would have been a great addition.
No one expected King Vorak to be mentioned given they're the first time a comic exclusive anything was mention in the show, which despite increasingly incorporating Expanded Universe content had ignored and increasingly decanonized the comics with Vorak's series being hit especially hard note The Dazzling's issue was straight-up made Canon Discontinuity, King Sombra's had its follow-up made Canon Discontinuity with his character ignoring the developments from his issue, Queen Chrysalis and the Changelings seemingly had their apperence retconned from battle injuries to being malnourished, Nightmare Moon's follows up the comic which treats them a separate entity from Princess Luna which the show and later comics would distance themselves from.
Viewer Gender Confusion: In the rousing speech between the different races, the pegasi are given one by what seems a filly...until they're voiced by a man. They had to later clarify they were male.
8 months before Endgame.