First off, Morrowind's system was not perfect and I am not advocating that BGS just change it back to that. That would be bad design. However, it had two things going for it which added to the game as a whole.
First - it added ambience. There were silt striders and boats and mage teleporters dotted around the world. They fleshed out settlements and just made the world a little bit more explained. How's everybody getting around? Oh, they're probably using the many travel services on offer. In Oblivion those vendors were missing and the world felt a little bit empty. In Skyrim they were there but they were... lacking. More on that in a bit.
Second - it made sense. Vvardenfell was a big place. Walking around took a while and was pretty dangerous. A low level character certainly wouldn't have been able to cross from one side of the map to the other completely unscathed using none of their equipment or potions. The travel systems they had in place in Morrowind provided an explanation as to why that was able to happen. In Oblivion and Skyrim you can zap to the other side of the map with next to no manual input. Not only does this hugely devalue all of the effort that goes into crafting the landscape, it also cheapens the act of crossing it. This is sad. It's led to a quest design system where 60% of game time is spent in linear, formulaic dungeons, 30% in towns and buildings and 10% actually journeying around. Those are not exact figures, but I don't think it's unreasonable to say that the game (and disc!) real estate being used up by the open terrain is being wasted.
So that's Morrowind's system. It added ambience and helped immersion (yes that word actually applies here). Don't care about that and just want the convenience of the Oblivion system because you're strapped for time in your life? Cool! That's fine! BGS can easily implement both systems and allow us to turn off the Oblivion option when we start the game. People who want immersion get it. People for whom it isn't a big deal can ignore it.
"What's wrong with Skyrim's system?" I hear you ask. Well basically it just showed that BGS has not been listening and does not understand on this issue which has split the community several times. First off: not having a fast travel vendor in every settlement made the carriages that are there completely redundant. Cool if I can get out to Morthal without touching the map's fast travel. What about getting back? I have to walk or use the map fast travel? Oh well that's just brilliant then. Problem solved! (not). DG added boats, but only to three major settlements which already had full caravan functionality. They are nice to have to add ambience as described earlier, but they don't tackle the bigger issue of ease of travel.
The system needs to allow easy travel between settlements. Both ways. Otherwise the problem persists. The travel vectors also need to be balanced across the world map so that the player can get within reasonable walking/riding distance of all of the corners of the map without using map fast travel. Walking is unrealistic for the vast majority of players. It takes too long and there are too many frivolous, unchallenging yet irritating little encounters on the way.
Now, TES6 should obviously adopt a more sophisticated system than Morrowind did. So, the basics remain the same but it gets a bit flashier. Instead of silt striders there are merchant convoys. They and the boats work like the caravans in Red Dead Redemption, whereby you can watch the landscape roll by or you can press a button, go to sleep and wake up at the destination. Minor random encounters and small minigames could spice things up a bit. i.e. you can play cards with the other passengers or guards or you can spar with people or you might have to help repel an attack or you might wake up to find the convoy has been successfully hijacked and you are now a prisoner and have to fight/talk your way free. The longer, possibly unavoidable random sequences would be proportionally less frequent and not come up when you're on a quest labelled urgent, but they'd add some flavour. They'd certainly add quite a bit to immersion. Edit: this could even play into factions warring between each other and local tensions such as bandits only appearing on a contended border for instance.
And finally, the last problem is the issue of backtracking. Nobody wants to have to walk back the way they came just to get into town to dump their stuff. Morrowind again had the answer and Oblivion again flipped the bird at Morrowind: mark and recall. For the uninitiated, these were two spells. 'Mark' marked a location and recall teleported you back there instantly. The most common use was to mark in the middle of a town and recall back when you were finished dungeon diving. I propose that TES6 adopt the same spells but also add scrolls or reusable items that fulfil the same purpose (slight tangent: with the reusable 'mark' item making a distinctive sound so as to make shopkeepers wary of people marking inside their businesses to warp back at night. Could be cool. Good reward for thieves to dabble in magic a bit but not punishing if they decide to refrain).
There we have it. A system which is plausible for getting the PC around a province fairly unscathed which adds flavour and ambience to the world which can coexist quite peacefully with the click-to-appear-there system currently in use (provided that there is an option to disable the latter system given that it's very hard to resist using in the same way an overpowered weapon gets nerfed when people complain it makes other weapons redundant). Can everyone agree on this?