Let's start saying that Boston or the other towns aren't to be removed according to my idea. They are still the starting place, and the harbour where you shall travel to other servers; The NPCs will stay there as well. Basically, it will be something akin to a starting area.
The overhaul first need some necessary steps before being introduced. Being able to produce flour at home is one of these. So, a millstone could be introduced that would permit to mill flour at home (probably with a large phlegm cost and a lesser output than a windmill).
In addition to that, personal and village stalls would also be introduced. Personal stalls can be placed on the edge of a personal claim (so that someone from the outside can interact) and offer a small inventory, while village stalls are placed by the mayor, that can also place a rent on them and a tax on the income (that would go fueling the village authority). They would also offer a bigger inventory than the personal ones.
Also, a postbox should be buildable on your own claim. More on this later.
Also, a new building would be introduced: the Hudson Bay Company offices. They would be placed semi-randomly on the world map (let's say, one every X maps, a relatively large area anyway, and not in the darkness).These would work as the npc stalls on town and here there would also be a banker and a postmaster, basically as in Boston and with the same functions.
And these were the preliminary steps. With these introduced, the teleport option would be replaced by a Hudson Bay Company menù, usable only from the homestead. Here you can access the npc stall options and suchs; you can buy from there and choose if you want the items/money delivered (for a fee, eventually deducted if you're getting money - and then you would find them in the postbox after some time) or if you want to get them yourself (and then you should travel to the nearest office, that could prove quite risky).
So, in short, this is what i propose. Having no more a central hub would place an incentive to make villages, especially if the village stalls are introduced as above - so making commerce a successful way to sustain a village. People that can't afford to go to the offices would have the item delivered and that would create a small silver sink. Offices would be a favored place for raiders, and so people would also need to patrol them for safety (and they could be paid for doing so). Basically, it would favor player interaction and the development of communities.