There's no way most of these even COULD be in Skyrim. They're (long gone) institutions specific to a very certain time and place. Like the Knight Orders, or the Order of the Virtuous blood. Those won't and couldn't exist in Skyrim, it wouldn't make any sense, there's no way.
It'd be like finding a Telvanni Tower in Bravil.
Quite true, many known factions simply wouldn't make sense in Skyrim, but that's fine because Skyrim gives us room to introduce new factions, being not only a different province but also 200 years after Oblivion, giving time for new factions to rise, potentially replacing old ones that are no longer around. I want to see factions that make sense in the game, and new ones are perfectly fine with me.
I expect to see the basic three guilds or their equivalent, if nothing else. Given the lore about the Mages Guild seperating into two factions, that actually allows for two Mages Guild equivalents in Skyrim, though that doesn't guarentee Bethesda will take advantage of it, it may be that by the time of Skyrim, one of these factions no longer exists, or it may be that only one is actually joinable, only time will tell, I don't think we know anything about what happened to the Thieves Guild or Fighters Guild, so there's room for the game to fill us in on that, the Dark Brotherhood has been confirmed, still, there's some other options left, one thing I'd like to see is being able to have the sides in the civil war as joinable factions, they could be similar to Morrowind's great houses, like those, you should only be able to join one with a specific character.
As to Umbra, I see no reason why it shouldn't return, 200 years is more than enough time for it to find a new wielder, after all.