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Redoran and Telvanni obviously, but will Redoran control all of the mainland featured? Or will the Stonefalls Coast region belong to House Sadras? Indoril has more or less merged with the Temple. Since Sadras is House Hlaalu's replacement and Balmora is going to be rebuild, I assume the Odai valley is going to be Sadras territory. This means that Redoran and Telvanni should control most of the territory in SoM, with Indoril only present as the political arm of the Temple, and Sadras being found in a few places but not having major presence in the Vvardenfell and Velothis Mountain regions.
How far north would Dres have been driven after the Red Year? Since Blacklight is the seat of the Grand Council they would obviously have an embassy and a cornerclub there. Would they have holdings on Vvardenfell at this point, after having lost so much to the Argonians? I'm waiting to hear what claims are available and in the meantime I hope to help figure out the direction of the world's design. I don't think Dres presence should be overdone by any means, but I think they should at least have a few representatives and allies present in Blacklight.
Suggestions for the current state of the Great Houses along these lines:
Redoran: Most powerful. Highly militarized, makes leading and protecting Morrowind its first priority. Friendly toward the Empire but values Morrowind's independence.
Telvanni: Remains strong after the Red Year. Highly reclusive wizards, holding to a might-makes-right ideology and involved in countless petty feuds and intrigues. Highly isolationist, doesn't truly adhere to laws but nevertheless makes its cases in the Grand Council.
Sadras: Replacing Hlaalu, Sadras is the enemy of Hlaalu and the primary target of their subversion: Hlaalu is technically a lesser house subservient to them, but has no respect for their authority. If House Sadras rose to power as a replacement to House Hlaalu, its goals would likely have constrast against Hlaalu's based on the attitude of Dunmer following the Red Year. Sadras would be considered a very honest Great House, ruling over the largest stable agricultural economy left in Morrowind and supporting free commerce between the Great Houses. On the other hand, it would be opposed to Imperial influence, even if it meant losing potential financial gains from Imperial trade.
Dres: House Dres would have lost most of its holdings during the Red Year, and so would be a shadow of its former self. House Dres will obviously hold extreme resentment against Argonians, and also against the Empire as well for its abandonment of Morrowind. As a ruined house, it turns to corrupt and violent conduct to manipulate the other houses. Its military and spies battle both Argonians and other Great Houses frequently.
Indoril: House Indoril was ruined even before the Red Year, and now it is basically a formal House through which the Temple is represented in the Grand Council. Indoril's governance on Vvardenfell probably extends only to the rebuilt Vivec City.
Hlaalu: The most corrupt and pro-Imperial of the Great Houses, Hlaalu has been off the Grand Council since the Red Year. They are now simply a group of families serving under House Sadras, which they work against in most of their actions. The Hlaalu are the go-to house for Dunmer who believe in profit above all else, supporting both smuggling and closer relations to the Empire when it suits them. The Sadras struggle to remove Hlaalu influence from most places.
Dagoth: The "Sixth House" of ash mutants lost its god, and with him their rulers the Ash Vampires. Its power no longer spreads through Blight, its Divine Disease no longer corrupts new victims. The Sixth House's remains consist of raving lunatics in the Ashlands, crying in vain for the return of their master and throwing fireballs at passerbies.
The most common alliances of the Great Houses:
The most common feuds:
Telvanni vs Indoril
Redoran-Sadras vs Hlaalu