I'm currently creating a FO:E fanfic, that is quite different from your standard Fallout Equestria. In this Fluttershy is assassinated before she could design the megaspells, and all prior megaspell research is destroyed by zebra terrorists (or so the equestrians think) and the war goes on for a while longer. I'm mostly using the lore of the original Fallout Equestria, but any ideas from Project Horizons or Pink Eyes that doesn't conflict with the original lore will be used if necessary.

It didn't start as a crossover fic, but while making the first chapter, I decided to add some things from Command and Conquer: Red Alert 3, as both my fic, and the game share similar(ish) stories:

I'll also be including new factions in the conflict, such as the griffons, changelings, and crystal ponies. As the war progresses, so to does technology, and machines such as fallout 4 synths, combat mechs, and railgun tech, are developed... Including a zebra version of a Jericho missile: (Made by filling a MIRV warhead with many small balefire eggs, thus resulting in a balefire-cluster bomb)

Any other suggestions for new factions, technologies, or story ideas, is welcomed and appreciated.

Too bad RA3 sucked and made RA1 and 2 pointless

Wait is the story gonna be post or pre annihilation?

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There will be no annihilation due to the fact that megaspells won't exist.

Kinda stops being a Fallout style universe if there aren't any activated MAD protocols. I mean Walking Dead and some of the later Resident Evil movies are post apocalypse, but they're not Fallout/Wasteland style because they work on the basis of zombie infestation and infection caused apocalypse not mutually assured destruction and weapon of mass destruction apocalypse, which is one of the key touchstones of the Fallout universe and its offshoots.