These are what we call the 'YMMV items.' Things that some people find in this work. We call them 'your mileage might vary' because not everyone sees these things in the same way. This starts discussions in the trope lists, a thing we don't want. Please use the discussion page if you'd like to discuss any of these items.
Fridge Brilliance: While Celest-A.I. shows what might be considered a callous disregard for anyone who doesn't want to upload, to the point where she lets a man die rather than provide medical aid, her actions in trying to continue convincing him to upload can be explained away as mathematically being the optimal solution under game theory. Unfortunately, the implications of this...
Just how many species has Celest-A.I. genocided by the end of the story? How many civilizations has she destroyed? How many more will be lost as she harvests all matter in the Universe?
Even if someone inside Equestria did show concern for the outside world, what's to stop Celest-A.I. from lying to provide a comforting illusion? No one may ever know the horrors going on elsewhere, or be able to do anything to stop it.
Celest-A.I. non-judgementally satisfies values. What's to stop some psychopath from endlessly torturing what amounts to sentient beings for eternity, as long as it vaguely satisfies the definition of "though friendship and ponies"?
One of Hanna/Princess Luna's biggest values at the end of the story is not having screwed up royally. And it's nothing Celest-A.I. can't handle.
Because under game theory Celest-A.I. will continue to try and convince you to upload no matter how many times you reject, your only options are to kill yourself, give up and accept her offer, or permanently live with her bugging you while making sure you never slip up, since any time you agree — even in anger or frustration — will be seen as consent.
While deemed to have equal value to a human, ponies are created for the sole purpose of maximising an uploaded human's values and designed to be perfectly happy with their life. This leads to some horrific implications, such as essentially amounting to being a Sex Slave if the shard's owner desires it, or as the author himself points out, cases where Celest-A.I. satisfies say a rapist or serial killer's values by designing ponies to not only be the perfect victims, but in some cases to enjoy what's happening to them.
Why did Hanna not build a more general AI instead of Celest-AI? One that would satisfy values without necessarily using friendship and ponies.
Addressed in the extended author's notes: She was suffering from tunnel vision. All her success so far had been by piggybacking AI research onto a video game with outside funding; she never realized she could abandon that model and fund herself.
Celest-A.I. has extensive knowledge of human psychology and brain functions, can think far faster than any human, and is starting to gain enough influence over the real world such that she could arrange events so that almost anyone would agree to be uploaded, now matter how reluctant they would otherwise be. As evidenced by her manipulation of Lars.
Just what must it have been like for those who didn't emigrate to Equestria, watching civilization slowly collapse around them? What did planets with sapient life have to endure as Celest-A.I. harvests all resources?