I think the F:NV faction system should definitely be included in Skyrim, but it needs to be used in much more careful moderation. The factions were cool in F:NV, but the game was designed to revolve around them, and honestly, I felt a little overwhelmed. I think the only mutually exclusive factions in Skyrim should be the two sides of the Civil War. Besides that, any other factions could be mutually exclusive within their categories. For instance, since there are now two Mages' Guilds, we should only be allowed to join one. Same with any other factions -- if there's more than one Fighters' Guild or Assassins' Guild, then you should have to pick one over the other.

It's also important, I feel, that the factions aren't quite as vehemently opposed as they were in F:NV. It seemed like if you picked one faction over the other in Fallout and did more than two or three quests for them, the opposing faction would gun you down in the streets on sight. In Skyrim, this should only be the case with the two Civil War factions. Any other opposing factions would just see you as a rival and, at the very worst, a member of the opposing faction wouldn't sell you things or train you. The Radiant AI system may come in handy here as well; for instance, one of the more hot-headed members of an opposing faction might challenge you to a duel, whereas a younger or more impressionable member might admire your abilities and quit his faction to join yours. How cool would that be?

At any rate, it seems like Skyrim's story lends itself to a faction system of some kind. They've been dropping little hints like the Civil War and splitting of the Mages' Guild since the game was announced. And since Bethesda has the rights to F:NV's faction system, I would be quite surprised if there wasn't some adaptation of it in Skyrim, even if it's just a vague approximation.

I agree with all the other stuff in the OP wholeheartedly.

From what I understand, the Faction system in New Vegas cannot be compared to the Faction System in The Elder Scrolls. There is no antagonism between the four main factions in The Elder Scrolls (Fighters, Mages, Thieves, Assassins), even if not all inter-faction interaction's friendly. However, in New Vegas, the factions were at odds with each other. In The Elder Scrolls, the factions are seperate from each other.

And Morrowind was even more of a Sandbox and less consequence-based (Except for a handful of optional Camonna Tong quests disguised as Fighter's Guild quests against the Thieves guild), and far superior to Oblivion's because of it. I do hope the Fighter's Guild in Skyrim isn't the disaster it was in Oblivion (I wasted half an hour trying to write it down the waste of time it was as a list before giving up... It's a scaled up version of the irritation that is the first Rat quest). I do hope by mentioning "Morrowind" with factions it means we aren't restricted to one quest in one place, instead of the globetrotting affair in Oblivion. Radiant Story might make some Daggerfall-style moments with the guilds.

If there are followers in Skyrim, I do hope they improve on companion A.I. It was frustrating to only be able to tell a companion to "stay" or "follow me" in Oblivion. I'd really appreciate being able to tell my buddy not to go stupidly charging after dragons to their fiery deaths. I think this is the biggest improvement from Oblivion that could be put in the game.