You'd think that's nowhere near a priority for refugee Dunmer in these times.
Why? People cling on to their traditions and beliefs, especially in times of turmoil.
Morag Tong killed people legally, they could do that because they where allowed by Morrowinds people in power. Outside of Morrowind they can't kill legally, since no other country recognize them as a legitimate guild. So Morag Tong wouldn't make much sense.
I guess the vampire clans could return, but they're about the only faction I can think of that would work, without too much work.
Some factions are there, but not expanded very well. I'd personally love to join the East Empire Company again.
The majority of Dunmer refugees are in eastern Skyrim, where the Stormcloaks hold the power, if you've travelled to Windhelm, you'll know that no officials care what the Dunmer do to each other as long as they stay away from the Nord population. Furthermore the Nord authorities dont do anything to help with any problems the refugees have. This situation is literally begging for organised crime to take over. Whether they are recognised by the country at large doesn't count for anything, see the Stormcloaks.
A faction related to administration of trade in the empire would be a welcome addition, in my book, but please don't call it the east empire company Skyrim is in the north of Tamriel.
Yes besides legion presence the Empire really has little to gain from a province like skyrim without exploiting its resourses. Remembering the Ebony mines in Morrowind. On that note I also miss the Imperial chapel mission that would still have its influence even without Talos.
THe reasons are strength unity and manpower. Just look at the great war, the only reason the empire wasnt totally crushed was because it had the allegiance of skyrim high rock and hammerfell at the time.
I can see Cyrodiil importing a lot of armour and weapons from Skyrim though, that would make a good basis for an empire trading faction