I think something along the line of the system used in Morrowind would work quite well in Fallout 4. You could go to caravans set up just outside the borders of most towns and arrange to go along with them. Perhaps there could be a random chance of encountering raiders or other hostiles. You could likewise perhaps use a jacked up underground railroad system. Either worn out trains or even just that thing you used when you go to The Pitt.
So long as I can still just simply fast-travel to where I wanted to go (with or without any sort of bonuses/penalties attached,) then I'd be fine with that. What I would
not want to see is something where the only way I can quickly get from place to place is to physically walk to a fixed location (caravan outpost/train stop/etc,) which will only take me to another fixed location. Unless we're talking about something where I'd be able to find a fast-travel "portal" at all of the boundaries of each and every outpost/settlement; along with an intricate system of travel routes that allows me to quickly get back and forth from all of the myriad little out-of-the-way places that make up such a large portion of a game like this.
Because that's something I was not a fan of in Morrowind - I'd do lots of exploring on foot, trying to uncover interesting places to check out. Once I got through some of the more extensive dungeons, however, I'd often want to return to a town to resupply and whatnot. And I never savored backtracking across a bunch of area that I'd already been through, just because there wasn't a nearby caravan/fast-travel access point. Frankly, that particular mechanic added little to my own sense of "immersion" and instead just became quite a big bother.
See, I'm very fond of exploring on foot - on the way out from a place. If I've never been there before, then I'm looking forward to seeing what's going to be over the horizon. I've never really wished in any of these games that I could fast-travel directly to a location that I hadn't already physically walked to. But what I really find a bother is anytime I have to make that trek more than once. I've already scouted out that area, and sometimes I don't feel like sightseeing - so much as I just want to get to where I'm going. And if I've already been there, and know that nothing interesting is ever going to happen along the way - then I'd really just as soon skip all the in-between.
And that's the problem I have with the whole "caravan" idea. (Unless it's only a totally optional thing, in addition to the regular Fallout 3-style Fast Travel.) It works great for getting from town to town - but I find in these games that I'm rarely doing that. If I'm in one town already, I'm much more likely to be heading out for some hiking around and looking to discover other places - places that these caravans don't usually stop at - most "dungeons" being at least slightly off the beaten track. And the times that I'm most likely to be using fast-travel is when I'm out in the middle of nowhere after a long run of exploring. I don't want to have to go to the nearest town before finding a caravan that will take me to another town - I just want to get to a a town. Once I've physically walked my avatar across the landscape to a place where I could pick up a caravan - the point is moot (because by then I'm already where I'd wanted to go, in the first place.)
If we're talking about adding different methods of travel on top of being able to compress time and "fast travel" (like in Fallout 3) through the more boring parts of the game; if it's just an optional thing for people to try out every once in awhile - then I'd be just fine with that. But I certainly wouldn't support making travel by caravans, trains, bus stops, etc, the only way of quickly getting around the world.