Labrynna Regime - As in previous submod incarnations. A large, well-established national faction, it's main problems are overcrowding, high unrest, food shortages and terrible external relations. The Twilight invasion and ecological damage from the Moonfall wrecked them, and even then the Flood took out half of their agricultural base, but enough survives to make Ambi's Regime a major power. Capital is Lynna, which is being rebuilt with some urgency as an administrative and military centre with the civilian population... somewhere else.
Tolemac - A federation of surviving Gerudo, Ordonians and southern Hylians, all settled on the low, fertile island that used to be central Ordona. Has enough territory to maintain horses/goats and the expertise to deal real damage with them, but has almost no standing infrastructure and starts without any national identity. Interim capital is currently Mesu Ordona, due to its proximity to nominal allies New Hyrule.
Gamelon - A coalition of Hylians who struck out into Airu's Reach rather than join the New Hyrule settlers, consisting primarily of merchants, minor nobles and skilled tradesmen who yearned for independence. Has almost extortinate trade revenues due to their business acumen, access to Death Mountain Range and stockpiles of Holodrum lumber, but have the same food and squalour issues as everyone else. Capital is the former Lanayru outpost of Seshei, which is currently unrecognisable due to all the hastily built town houses and warehouse districts.
Koridai - A Gerudo watch station on their northern mountain border, now filled out with Daira, Zuna and even Hylians from Bandits Cove. Is cultural and pragmatic enough to dodge most unrest issues, with a relatively large army and stewardship of the remaining northern desert, but is utterly unprepared to maintain even a fraction of its current population. Capital is the camp on the shoulders of Mt. Koridai, which is now an active volcano (again).
Arcadia - Turns out Majora missed a few (hundred) Deku Scrubs, and they have joined with the starving and homeless Lizalfos and some renegade Kokiri to maintain whatever's left of their respective homelands. The newly founded Arcadia includes the remaining isles of Kokiri Forest, the ridge of northern Lost Woods, and has made inroads into Death Mountain. Has a handy and mobile military with some room to expand, but must first manage serious logistics issues, an impossibly wide three-way cultural divide, widespread infighting and the interest of various other parties for whom Death Mountain is available. Capital is a former hunting camp just above the Sacred Forest Meadow, which bears the lost settlement's name.
Zora Restoration - Prince Ralis' bold, if poorly planned and provisioned, expedition to reconquer Dominion Valley and attain the old glory of his father's kingdom. Formed from Ocean and Lanayru Zora, with little regard for purity of blood in the present circumstances. Starts with only a ruined and undeveloped Kakariko and a very poor administrative system, but has a considerable initial force to play with and has the potential even to rise to the level of pre-Moonfall empires. Also is less affected by the ravages of flooding than most factions. Capital is Kakariko Village, based mainly in the submerged sections of the town, and by the request of the surviving Sheikah they will not touch anything that may float out of the Shadow Temple.
Cult of Holodrum - A part religion, part ecoterrorism movement maintained by various surviving Fairies, Horonian Mystics and those Subrosians caught on the surface. Based in the almost unscathed forests of northern Holodrum and Natzu. Prefers powerful stealth-oriented magic units who are screened by hordes of untrained humanoid dupes, and their combined determination gives them a sense of unity, but their remaining territory is barren and their greatest enemies (Labrynna, Gamelon) will likely look in their direction to expand. Capital is Natzu, where the remnant Great Fairies continue to hide from (and usually capture) the occasional unlucky sniper.
Darknut Legion - As described in previous posts. Having more or less survived the Moonfall and Flood unscathed the Darknut have to deal with incoming refugees, the near-extinction of their client races, the deposing and death of their living god, the loss of their most distinguished warriors in the fight against Majora and the risk of revolution from the new generation of Initiates. Capital is still Ontheon, in which King Senturon considers his alliance with the Keatons and, perhaps, the birth of Zuna gunsmithing.
Calatia - Formed from Gorons either too stubborn or too involved to join the search for their lost brethren into the Great Sea, plus the Hylians who fled to them rather than anywhere else. [Still need to think up a mood for this faction, plus their location / capital / advantages and disadvantages]