I think I'll separate the seasons into different stories. That way, I can continue with the series even if I reach the IDW comics, which is still in progress and takes place between seasons 2 and 3. That and also so I can make a lowdown on my original character's abilities and such.
Future of Shisno Chronicles: Friendship is Magic
I'm not done with the first series yet, but I figured I'd come clean with what is soon to come.
SC:FiM: The Return of Harmony
Covers the titular Season 2 premiere. Will be not only in Chronicle's POV, but centered on him. Warning: Start of an OC/canon ship and Discord-bashing.
Comes in three parts (which may or may not be split into their own parts): The Rise of Disharmony, Chronicle's Promise, and The Wounds That Remain.
Shisno Chronicles: Friendship is Still Magic
Covers Season 2 from "Lesson Zero" to "A Canterlot Wedding", an includes an extra chapter prior to that that will cover one of the consequences after "The Return of Harmony".
SC:FiM: The Return of Queen Chrysalis
Covers issues 1 to 4 of the MLP IDW comics.
SC:FiM: The Adventure Continues
Covers Season 3.
SC:FiM: The Nightmare Forces
Covers issues 5 to 8 of the MLP IDW comics.
SC:FiM: Equestria Girls
Covers the tie-in movie.
The Mane Cast (Mane Six + Spike), Derpy Hooves, and an OC are sent to the Team Fortress 2 universe.