I think this man (a game designer at Epic apparently) nails why such things as fast travel and regenerating health can be so disconcerting: http://gamasutra.com/blogs/AdrianChmielarz/20130423/191043/Why_the_NextGeneration_Will_Change_Games_Forever.php
His basic thesis is: There are two types of games. A "game" game, a toy game where everything is abstract and purposefully silly and very much not trying to drag you into another world in terms of escapism. EG the Lego games and Mario and etc. Games where nothing is supposed to be or feel "real".
The other end is the "sim", the type of game that does try to svck you in, that does try to place you as someone else in a different world. This sort of game specializes in making you believe in its characters, and tries to get you to believe in the world its presenting as some other place your in, and not a toy you mess around with. This sort of game needs explanations for why things happen, even if they aren't based in reality there still needs to be an explanation for why your health regenerates, and how magic works, and people will notice and wonder why others don't have regenerating health?
And The Elderscrolls has become stuck in the middle of these two. It's become more and more "toy" like, with regenerating health for no apparent reason and fast travel that just blinks you back and homes you can just wander in and take everything. And yet it hasn't lost its "sim" aspects, of trying to get you to believe you're in another world, and that this place exists, and trying to get you believe in different characters.
And for the most part I agree with the man above about the two different types of games feeling weird when the mix too much. When you got to see others in Bioshock use things like Plasmids, and see its effects, and have vending machines with them everywhere, and have them as part of the story they worked well. You didn't care that they were fundamentally silly, because they were built into the story and gameplay enough that you could easily accept them. The vigors in Bioshock Infinite didn't work nearly as well, they felt out of place, because no one else used them and they were barely acknowledged story wise.
Looking back, I can see the same sort of problem occurring with Skyrim versus Morrowind. People have named Morrowind as better, at least partially I can see because many more of the mechanics at least tried to have an explanation. Even if you could steal things right out from under NPCs they'd at least try to catch you, and fail because of the eras AI and not because they're designed not too. Being able to heal had an explanation, being able to travel quickly from one place to another had an explanation in the game, in the story, you could believe in it.
But Skyrim has so many thing that you don't have an explanation for. Why is it I can shoot an enemy through the head with an arrow and he doesn't notice? Why is it my health comes back for no reason when no one else's does? That these mechanics might be more fun is besides the point of not offering up an explanation, and so not making people believe in the world presented.
So for the next Elderscrolls, indeed for any game Bethesda makes, I'd be hopeful that the above blog would be a thoughtful and useful example of what to keep in mind. Is that game a toy, a "gamey" game? If so then make sure everything likes up with that. Is it a sim, a thing that draws you into another world? Then make sure the game mechanics all line up with an at least semi plausible story explanation and mechanics that seem to make sense in that world. Have a reason for all these things, have the world be coherent for the player and they'll believe in it more. Don't get stuck in the middle somewhere not really doing either end of the scale.