Creator Backlash: The author cringes while reading Post Nuptials, and his readership complaining that his newer entries aren't as good as the first has not helped. His main complaints are that it's far too repetitive and, at times, stilted for its own good. In fact, he's keen about the idea of an AnimatedAdaptation Distillation of his work, so long as he's the one to pen it.
Metamorphosis and Honeymoon were written as chapters for Post Nuptials, but were released as standalone stories since the author felt they would have detracted from the subject of Twilight's friends walking out on her.
The author decided against shipping Rarity with Fancypants and Fluttershy with Iron Will, because both seemed unnecessary and the readership was also against the idea.
Shining Armor's chapter would have had him speak with Cadance instead of Twilight.
Post Nuptials would have ended with Rainbow Dash and Pinkie moving Applejack and Rarity into the same bed as a prank. A similar ending showed Twilight's friends finding Octavia and Vinyl Scratch sleeping in Twilight's bed while Twilight slept with Celestia. Both were nixed to keep the story friendlier for younger audiences.
The story was planned to be focused only on Spike, and went as follows: Spike learns of a magic pool that will let him see anything asked of it. He wants to see his parents, but Twilight forbids him from going, so he runs away. As Twilight searches hopelessly for him for a month before finally giving up, Spike finds the pool guarded by a character who would become the main story's Keeper. He asks to see his mother, and what does the pool show him? None other than Twilight.
After the above was changed to the plot that was actually used, the story was going to have a scene at the end where Applejack realizes that Pinkie's right and she does have a crush on Twilight. This would have led into a story focused on AJ dealing with it, with tragic results due to Twilight being straight. However, the author decided to scrap that idea, and the scene wasn't included.
Word of Gay: According to Darth Link, Rarity, Fluttershy, and Cadance are bisexual, Applejack is gay, and Pinkie is asexual.