Skyrim already showed that Bethesda was struggling to 'continue' the story, since the continent has been in peril quite a few times already. You can't really keep saving the world all over again without it getting somewhat dicey in the lore....


So there's a few things i want to suggest, both can be taken independantly:

1) Move the setting off Tamriel and onto another continent. There's bound to be some interesting places to visit - Some of which we've already heard of in the lore. My idea here is to take it up a notch, literally.
Some of you probably know the Eberron D&D setting. It's got a pretty interesting city: Sharn. Basically, the city is vast, but not horizontally. Instead, it goes down deep into the earth and up high over the clouds. Rather than situating a TES game across a vast landmass, it might be an idea to situate it in such a city?
The faction interplay there would be obviously pretty interesting, people and groups vying for power over this metropolis.
The lore background would be quite fascinating aswell, as there's not many civilizations who would have been able to build a city like that, but more to the point, why they did it. Might have something to do with the geography at the time it was built?
Of course, this would raise the issue of the races. Would they be there at all? New races? Maybe the city is actually something in the far future of Tamriel, though that may resemble Sharn too much for comfort.


2) This is Rather than making the story about 'the end of the world' like in every other TES game, make it about the protagonist and his/her role as an "emissary" of the Elder Scrolls. You start in prison, but how or why no one remembers, as if you've been put there and forgotten straight away, thus removing the direct influence of the captors like in the previous games (since you don't actually serve their fate but your own this time). Instead of filling in the blanks afterwards, you simply don't know where or what you are, and how you got there. It's almost as if you just sprang into existence on that spot...
Naturally, you somehow get out. Maybe the guards just let you out, you're there by mistake since obviously you haven't done anything - The guard who supposedly put you there turned out to be corrupt. This might start the secondary main quest, as a hook to find out what's going on in the area where the game plays.
Eventually, you get more and more clues about who - or rather what - you are. This main quest would be completely without the 'time limit' of other, past main quests. There's no big evil to stop before it destroys the world and it can be done at your own pace, giving you much more opportunity to simply do what you want rather than feel pressured to continue the main quest (though i admit this is a personal gripe of past TES games).
I wonder whether i should put spoiler tags here, but on the other hand it wouldn't serve a purpose if this idea would never get used. But the story pans out in what might be an intruiging way:


Just ideas, but i felt i should put them somewhere...