If there's ever a third visit to Innistrad, one possible story hook is all the religious schisms in the wake of Avacyn's death, learning the truth of her creation, and the Eldrazi incursion. No single faction is strong enough to win outright, and strange alliances form and dissolve every day.
The set's factions are enemy-colored, an inversion of Innistrad's usual ally-colored creature tribes, to reflect the dissonance and upending of all the usual alliances. There's a lot of untapped potential in this- the only specifically enemy-color set so far has been Apocalypse, all the way back in 2001.
The overall mechanic identity of the set features a lot of choice, whether in modal cards or designs that are useful in multiple archetypes. Perhaps there is a cycle of “schism” enchantments, like the Sieges from Fate Reforged, representing the two factions associated with each color.
White/Black- Children of Markov
The truth about Avacyn is now public: she was not humanity's savior but a game warden, created by Sorin to balance the ecosystem (and ensure a stable food supply for vampires). Many people reject this as heresy, but the Children of Markov believe and embrace it. Its members are mostly humans and vampires, seeking to reconcile the two species.
Its mechanical identity focuses on sacrificing for the greater good, and universal effects (whether positive or negative.)
Blue/Red- The Galvanic Cabal
The Cabal holds that revering angels and demons and elementals will only bind Innistrad to its miserable past, and that scientific inquiry is the best way forward. They study lycanthropy, geists, demons, vampirism, but above all necro-alchemy. Banned scientific texts arrive in Nephalia's ports every day, to be copied and tested and expanded upon.
Its mechanical identity focuses on jolting the dead to life, looting, controlling many different permanent types, and creating Clue tokens.
Black/Green- Pact of the Crossroads
Ancient forces stir in the wilderness. Demons, elementals, and beings utterly unknown offer immense power to hermits and outcasts. Members meet on backroads to exchange gifts and secrets. Many members are werewolves, already familiar with the deep wilds and its denizens.
The Pact's mechanical identity focuses on resource conversion, power at a cost, and knowing when to take a calculated loss.
Red/White- Heron Corps
The only problem with Avacyn's incendiary purge was that it was cut short. The Heron Corps are the most militant and organized faction, claiming direct continuity with the true Church of Avacyn. Doubts and worries are drowned out by marches and slogans. They regularly fight and ostracize rival factions, but spend plenty of time turning on themselves.
The Corps' mechanical identity focuses on going all-in, punishing and hosing opponents, and never backing down.
Green/Blue- Writhing Union
Emrakul is now sealed in the moon, but trace amounts of her power still seep out. The Writhing Union seeks to release her, binding all of Innistrad in beautiful ecstatic unity. They build temples on the strongest concentrations of her influence, cultivating mutations through the generations.
The Union's mechanical identity focuses on transformations, with incentives for playing many double-faced cards.