As you know, Bethesda finally released the mod creation kit for Fallout 4 and the good stuff is about come in due time.

But in case some certain modder is a member here (Unlikely. But we can hope) I might throw this idea on the table for a mod idea or a fic idea.

First, there's already a anthro pony mod you can find on the New Vegas nexus
Second, Fallout 4 spoilers ahead. Proceed with caution

You already know about the Institute, "The Boogeyman of the Commonwealth" as many people call them by. Kidnapping people and replacing them with Synths (Androids), Shadowy goals that spawned enemies like the Railroad, the Brotherhood of Steel arriving the in Commonwealth, and the Minutemen, treating their synths as slaves, and other questionable actions. But above all they want to save humanity at the cost of Commonwealth. But what if there was one scientist that wanted to create 'Unique' Synths that's more Equine looking than human.

This brings up a MLP shout out reference when you go to Wilson Atomatoys Corporate HQ located west of Diamond city.

and for shits and giggles, there's a super mutant named Big Mack located in Atomatoys factory and he's not a mutated earth pony. Also...

Anyway, Imangine this scientist was a secret Giddy-up Buttercup fan and wanted to continue Arlen's idea but using the institute synths as the foundation. However, many of the scientists will laugh at the idea and saying stuff like "We're scientists not toy makers.". But Father the leader of the Institute might give this guy a chance to prove this idea can be beneficial to their cause and so he did. He planned to make two gen 3 synth horses but when he created them, he accidently gave them human bodies and resulted them being anthros. For the two, they are synth version of Celestia and Luna. But he developed an emotional connection with them as in father and daughter relationship, and worry about what will the Institute do to them. He chose a bold move by leaving the Institute along the synth Celestia and synth Luna and find a place in the wasteland so they can live in peace and possibly create more anthro synths. In the end they found you, the Sole Surviour of Vault 111 and moved them to some settlement that you and create your own synth like in Automatron (I want a build a synth mod now, please).