Yes I know all of that, but why do they hafto be Morrowind specific? Why cant there be a lore friendly way to introduce them to Skyrim? I mean since Red Mountain exploded, whos to say some of these guilds didnt pack up and dip out, re-establishing themselves elswhere (And I dont mean the Khajiit homeland..lol) Because I mean, the Dunmer in the grey quarter even talk about how they left Morrowind and walked west until they reached Skyrim..Perhaps some of the factions did the same?
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.