YMMV / The Conversion Bureau: Not Alone
Starman Ghost himself states Not Alone was written to set right perceived issues with certain other TCB stories. Whether or not certain story plot points are established by fiat, have or lack substance and make sense are things that have divided the readership.
Starman Ghost's own decision to delete the story from Fimfiction.
Ho Yay: Between Andrew and Ice Breaker.
Misaimed Fandom: Readers who defend the humans putting ponies into internment camps. The author has said in comments that they're supposed to be an unjustified, kneejerk reaction motivated by racism and paranoia.
Fans who want to see Equestria glassed. They don't get their wish.
Also, fans who want to see all of humanity ponified and brought under the control of the Equestrian Diarchy. They
really don't get their wish. And the readers that don't seem to quite understand the fact that the story is a Deconstruction Fic that runs on Grey and Grey Morality.
Patrick Stewart Speech: Arguably, the entire story is one of these to the original. Possible examples include the EFH posters and the declaration of war speech.
Tear Jerker: The entirety of the chapter titled "He's Dead." Aside from being a tearjerker, it also outlines the exact Fridge Horror issue of the personality changes that come from the ponification.
Andrew is forced to lie to Thunderhead to make amends. It's the first time Thunderhead's been happy since his "birth," and it's not even true.
The Woobie: Poor, poor Thunderhead. Imagine if you came into being at someone else's death.
Andrew/Iceman as well. He's lost his best friend only to have him replaced with a crude caricature.
The ponies involved with the EFH as of "The Longest Day". After Bon-Bon outs them, it's decided that they have to leave Ponyville.
Of note are Cheerilee, who is no longer trusted to teach the town's foals, and Mayor Mare, who is removed from office.