What Could Have Been: Word of God is that originally, there wasn't going to be a whole series of stories, but rather just Mare of Steel. It would have continued past the second arc to Rainbow Dash and the other Mane Six fighting off Darkseid, with the fallout causing Rainbow Dash to go into self-imposed exile. Then there would have been a Time Skip, followed by adaptations of Superman Returns, Superman vs. the Elite, and The Death of Superman before finally finishing. However, the author was inspired to write a whole series of crossovers, so those plans were scrapped.
The Red Kryptonite side story was supposed to also feature Twilight tinkering with Pink Kryptonite, but that was cut.
Mare of Steel was originally going to have a third Sequel Hook, with Batpony calling a meeting with Rainbow Dash and Diana (who would have met offscreen) that lays the groundwork for the Justice League. However, due to wanting to avoid Ending Fatigue (and having not written the crossover story that had Batpony and Supermare meeting yet at that point), this was scrapped.
Dark Knight Over Trottingham had some story issues, since it technically is the first story in the universe (aside from the War in Heaven backstory), particularly over Blueblood's capture by Zod. The author wasn't sure how to make the story work in that timeframe, and even considered retconing the dates. However, thanks to a fan suggestion, he found a way to harmonize the timeline so he didn't have to change the dates.