What Could Have Been: Originally, the author planned to end the first story on the 20th chapter, with all victims of the war returned back to life and, in the case of griffins, reformed for better, due to the influence from Elements of Harmony. Ultimately, he rejected this concept, thinking it would render the entire plot meaningless up to this point.
One of story concepts was to make the Mane 6 as the main characters of the story and make all of them fly planes, as in actual Ace Combat games. However, the author decided to give the main roles to Rainbow Dash, Fluttershy and some background pegasi, feeling the background characters from the show were "underappreciated" and he hoped to make the story a bit more original when compared to other Ace Combat crossovers, such as "Ace Combat: Shattered Rainbows" or "Ace Combat: Battle for Equestria".
Word of God: According to the author, The Equestrian War is the first story of "Ace Combat: Equestria Chronicles" mini-series, which will contain two stories or a trilogy, provided the second story will be somewhat popular.
Recently, he confirmed that the plot of Ace Combat: Wings of Unity will partially revolve around The Crystal Empire, but the Changelings will not appear.
The griffin soldiers are known only by their codenames and most of them have real life names. The author plans to reveal them in the sequel (some have already been revealed in the spin-off "Ace Combat: Gryphon Wings").
The dragons, specifically Aigaion and his Drake Generals, are based on various airborne fortresses featured in Ace Combat series, right down to their names and methods of attacking (aside from regular dragon fire).
Recently, the author confirmed that the stories are placed within Ace Combat Strangereal timeline, with The Equestrian War happening between 2018 and 2019, the spin-off Gryphon Wings occurs between 2019 and 2020, while Wings of Unity occurs in 2021. It may explain how the EAF was able to construct another Atmos Ring.