I recently came to the conclusion that unlimited fast travel is a rather cheap move gameplay wise. Paying for transportation to the nearest town and then walk to your destination makes much more sense immersion wise. Then again, when I remember Skyrim, reaching a quest location just to get back near for another quest an hour later can prove frustrating without fast travel.
In the end if there are waypoints to travel to by caravan or whatever are decently placed around the map and paths to walk are clear enough to distinguish then I would prefer this system over simple fast travel.
Adding Vertirbird to the mix (with a cost) would spice things up, too. Though I believe this stuff will likely be used on the main quest and maybe a BoS storyline. Otherwise it might be a balance issue, as I assume that the vertirbird has weapons that you can use, i.e. the minigun and rockets.