The areas left out are:
Stros M'Kai and the entirety of the nearby peninsula
A good chunk of western Skyrim is split between unused land in the north and apparently belonging to Cyrodiil in the south
Soulstheim
Almost all of Vvardenfell (And the lore forum breathed a sigh of relief)
An island the size of Soulstheim to the northeast of Morrowind (can anyone name it? I can't)
Most of the Telvanni lands on the mainland
Almost all of Black Marsh (thank you knahaten flu)
Anvil, Kvatch and the surrounding countryside,
And for the Dominion, absolutely no land is left out.
I must say, it looks as though the Pact is getting the shaft. The largest of the areas left out are canonically unexplorable for two thirds of the Pact at this time anyway, so if it is for lore purposes that they are left out it's quite ballsy of Zeni and I applaud them. This may also be an effort at balancing the Ebonheart Powerhouse by leaving out most of the cool stuff that people want to go see from the main series, to be added in later once player populations have cemented themselves in the other, less popular factions.