How would Equestria possibly beat humanity in a all out war? Sure, Unicorns can cast spells fast enough to act like guns, but that's only a third of their population. Humans have artillery more powerful than anything we ever saw in the show.
How exactly is Equestria going to support (as in feed and house) an influx of millions, if not billions of new residents?
The Calm Before the Storm side story for The Conversion Bureau: The Other Side of the Spectrum gives us the very clear answer: they can't. The Solar Empire is already taxed by the war and can't shoulder the influx of two billion newfoals. The environment is in shambles due to rapid industrialization (to provide jobs for the newfoals and churn out new war machines), the newfoals live in horrible poverty (and are often exploited as slave labor) and there are massive food shortages going around too.
It also addresses more Fridge Horror: The Barrier is destroying any of the human infrastructure they could have used to actually support them.
Chatoyance's stories have earth under the rule of a Mega Corp. on par with Buy n Large. Considering the backstory was that the economy completely collapsed and not to mention the fact that there are 196 countries in the world (who all have their own governments, systems, traditions, etc.), how exactly is this set up going to work? Artistic License – Economics does not even begin to decribe the massive leaps of logic this will require.
Considering Equestria has plenty of other sapient species (donkeys/mules, cows, buffaloes, Diamond Dogs, dragons, and gryphons), what do they think of an entire species being forced to become ponies?
Some stories have Equestria just randomly popping up in the middle of an ocean. Where did all that displaced water go?
The Conversion Bureau: The Other Side of the Spectrum actually addresses this, even having Twilight going off on the scientific reasons about exactly why this is impractical. Besides the massive amounts of magical energy it would take to transport an entire continent to another dimension, that is. Here is said rant, reproduced with all links in the event that you are curious:
Why doesn't humanity do some kind of space program (make ships where a decent sized group of people can escape the earth before the purification spell hits)? And then you wonder But What About the Astronauts?...
How can ponies claim that Humans Are Bastards and that "Ponies are the Superior Beings, incapable of doing wrong," when we've seen ponies (and other species in canon) act in ways that are remarkably antagonistic, including the Mane Six?
Moral Myopia. Remember, they're committing genocide without really considering the repercussions.
It's usually also Fanon Discontinuity, especially with Chatoyance's work. She rejects any part of the show that doesn't fit with her ideals, including the times when ponies show that they're just as flawed as humans.
Chatoyance's world has technology being destroyed by magic, yet her potion is explicitly stated to be a mix of nanomachines and magically charged liquid. Why doesn't the magic from the liquid destroy the nanomachines and render the potion useless?
She also has the human killing techbane barrier being deliberately created by Celestia,so maybe that tech was made an exception to further her plan, or they just made it outside of Equestria, as only the barrier magic is said to mess up technology
Recombinant 63 (a prequel to her TCB series), finally revealed the answer: To prevent magic from destroying the nanomachines, they used magic to construct and power the nanomachines.
The conversion serum is stated to cure many diseases and genetic conditions and handicaps. So why don't the scientists and ponies find a way to make a cure for these conditions without requiring the changing of the drinker's body and mind?
In just about all imaginings of the TCB universe, magic is stated to be harmful to humans. However, the potion is a magically charged liquid. Wouldn't the potion itself be lethal?
Plenty of things are harmful but don't have immediate effects. If the potion turns them into a pony before the magic kills the human, they should be fine, for given definitions of "fine".
In Chatoyance's stories, religion is evil. Yet the ponies are, in essence, a highly religious society, as Celestia is an object of worship.
How does the barrier distinguish between human-made things, which it vaporizes, and natural things, which are left untouched?
According to Chatoyance's story The Reasonably Adamant Down With Celestia Newfoal Society!, which takes place several years after Earth was destroyed, over 50% of the human race died, mostly from apparent mass suicide (note that by this point, the world population was roughly 18 billion). Even worse, most of the survivors are indicated to be from the last holdout regions who were forcibly converted by World Gov emergency response teams.
Most Conversion Bureau stories only mention the United States and make it sound as if it's the only country. Although it's most likely a case of Creator Provincialism due to most writers of these fics being American, it still brings up the question of what possibly became of the rest of the world. It's made even more horrifying when you never hear of people outside of America being offered the chance to be "ponified."
Several fics take place in Australia, a couple in South America, and many allude to the European bureaus. This example is mainly a result of the earlier days of the 'verse when things weren't mapped out as well yet, and authors focused on their own settings.
In Chatoyance’s 27 Ounces, it's stated that two ounces of ponification serum is the absolute lowest amount that has been successfully used for conversions, with anything less inevitably resulting in a horrifying and painful demise as the subject is only partially transformed; three ounces is the official dose, for safety reasons. While usually ingested to ensure proper effect, contact alone is all this is necessary. Later stories see the serum used as a spray for the purpose of mass conversions. In addition, the PER has weaponized the potion in the form of specialized ordnance. In one case, they used squirt guns. It's not at all difficult to imagine how often these less-controlled methods of delivery would fail to add up to even two ounces of total exposure. In that case, the PER was probably responsible for many more deaths than the HLF.
Celestia seems very nonchalant about exterminating an entire species. In addition, many TCB fics ignore the existence of Diamond Dogs, gryphons, dragons, etc. Does that mean Celestia already exterminated the other sapient races that inhabit Equestria?
What about the animals on Earth? Something that would destroy all human life would have no way of differentiating between humans and, say, monkeys or bears. The barrier also destroys human made structures, which means that all of the human constructions designed to prevent disaster would fail THE MOMENT that the barrier reached them.
And that's not even getting into the nuclear power plants! The barrier would destroy the buildings and reactors, letting loose a lot of radiation, killing and/or horribly poisoning anyone for doing something as simple as breathing.
Building off of that, nuclear waste. It's usually (mostly) safely contained... in human-made structures. Barrels holding the stuff would vaporize as the barrier hit them, spreading their contents across Equestria.
There are a lot of authors who see the pony genocide as a good thing — usually vehemently defending their viewpoints and/or cheering the ponies on. The fact that they are celebrating a deliberate killing of humanity sends some verydisturbing messages.
Something I thought of after seeing Inside Out: In Chatoyance's fics, Newfoals can feel no negative emotions. But all those negative emotions have a purpose. For example, without Disgust, they could, say, eat Pinkie's baked bads until they died of food poisoning, because Disgust is the way the body tells you 'Ugh, this is bad and possibly poisonous. Stay away!' Without Anger, they'd be total doormats, because anger prompts people to defend themselves against unfairness. Lack of Fear would cause a somewhat similar effect to leprosy - the purpose of fear is to tell you when to get out of a dangerous situation, so without it, the Newfoals wouldn't be able to keep themselves safe. And the entire point of Inside Out is that Sadness has a role too - it aids in empathizing with others, and it's how one signals that he/she needs help. Without it, one would have a Lack of Empathy and no way to tell others that they have problems. What's happening to the newfoals isn't 'being uplifted to a happier state of existence', it's severe emotional lobotomy that should leave them completely unable to function in the world.
Newfoals are often left as unable to feel anger, which would make them Extreme Doormats. So what happens when they try to raise children? Pushover Parents wouldn't even begin to describe it.
The Conversion Bureau: Conquer the Stars shows the consequences of this. It's part of the character Firebird's Freudian Excuse: Her Newfoal parents just couldn't deal with her firey attitude and couldn't accept her cutie mark (crossed swords over a shield, which she got defending another kid from being bullied).
Celestia is dramatically more powerful and has a different personality than her canon self. If the Gods Need Prayer Badly trope is in effect for the Conversion Bureau universe, this actually makes sense: Celestia multiplied her number of followers several times over in just a couple short years, so she's riding high on an ENORMOUS power boost.
Well, to be fair, part of this is because the majority of TCB stories were written around the first season and earlier parts of the second season where we've never seen Celestia's limits (and well before Lauren Faust herself said that, as far as she was concerned, Celestia and Luna aren't goddesses). A minor number of fics later on noted this and some have changed the barrier into a spatial anomaly in order to nerf her.
It's been noted that, since ponification changes one's mind, body, and soul, the resultant pony should rightly be considered a new being that simply possesses the memories of the original human. What nobody's ever considered is that the ponies have promised as much in the style of "To Serve Man". When they say that ponification "makes you a better person", they refer to the fact that the conversion process takes a human and uses their physical matter to literally make a better person.