Practically speaking it's not really possible to have different parts of the map that only have a couple of narrow access points
Why not? Geographical choke points are what "choke points" actually are.
it's a huge open world that is procedurally generated then hand tweaked. Hand crafting a world this size just isn't practical for an indie studio, so we had to take a compromise route.
Fine, so use your procedural generation to generate your world according to the generation rules you supply. i.e. make the generation include generating the chokepoints.
Types of chokepoints include:
Narrow land bridges between bodies of water (like Istanbul is built on)
Any other river crossing (man-made bridges, or low points in the water during dry seasons, or just slower water)
Narrow lushland paths between bodies of desert (check the current ISIS and Syrian wars - they follow the rivers)
Mountain passes ('cause nobody could ever cross the alps)
Rocky cliff-like regions where the only route is through canyons or between large rock outcroppings (this is kinda like mountain passes, except the "mountains" are smaller, and the passes are at, or below, ground level)
Cave tunnels running under mountain ranges
Natural pathways going through valleys and around hilly areas and around forests
Basically any path following something (like a river, or a cliff wall, or the edge of a forest), or any area that goes between two rougher or uncrossable areas of terrain (like being caught on a beach between a cliff and an ocean)
I was thinking that I can apply specific access points for trade via roads, which is kind of the angle I'm going with now. I have npc cities and player run cities, and the general idea is you have to transport your goods from your player run city to an npc city to be able to sell to players outside your guild. To transport your goods you have to stay on a road. If you are on a road you can carry a lot of weight, if you go off, you become extremely encumbered.
That sounds artificial. Why would you get more encumbered by going off-road? Perhaps I misunderstand how you are using the word 'encumbered', but often in video games 'encumbered' is shorthand for 'weighted down'. Why would your cargo weight increase when off-road?
Why not just increase your movement speed ~10% on common paths (like dirt roads), and ~25% on really good paths (like stone roads). And your game can even dynamically change to 'create' new paths through constant player use (if players start taking another route) and 'erode' old paths through disuse. Sure, it doesn't make much sense for a dirt pathway to gradually turn to a stone pathway, but since it's not happening all at once before players' eyes, but over a period of real-life weeks, it could fit the lore through willing suspension of disbelief.
Or better yet, why not make the non-paths actually take more time naturally without artificial limitations in some way or another?
Here's two ways that it function in real life:
Rivers often became "highways" because boats move alot faster and more predictably on water than humans on land. Rivers are natural chokepoints. Piracy is naturally fun. Magi-empowered piracy even more so.
Humans can cross almost any terrain (limited by some obstacles like mountains and such), horses can cross less, and caravans can cross even less. By making horses naturally unable to navigate in some areas (without artificially hindering them), and by making caravans even less maneuverable terrain-wise, you got your chokepoints and more player choice (do I carry a backpack of goods and go an unpredicted route? Or risk a horse-load full of goods (perhaps with a secondary packmule as well) and go a more risky route? Or do I take a full wagon of goods, but go a route that is pretty much guaranteed to be monitored? If I take a wagon, should I hire some players/mercenaries to escort me? Or will they turn on me half-way to my destination?).
Even boats on oceans tend to follow common paths naturally by humans taking the straightest route for economic sake, or travelling in convoys for security.
To make things more interesting I was going to put a couple of watch towers on the road between every player run city and the npc cities, and watch towers are also player controlled.
It's funner (if possible!) if players choose where to build watchtowers. And ofcourse, watchtowers can be destroyed and captured. And even if they aren't destroyed, they still have to be manned. And nothing (part from other players' actions) should prevents highwaymen (or local barons) from building watchtowers to setup tollhouses.
I would definitely try to set up rules to generate the terrain you want, to encourage the gameplay behavior you want. I don't have experience with procedural generation, so I don't know how to do it, but I've read enough to know it's possible to do it.
Secondarily, I'd try to run code on the terrain after (more specifically, during) generation to detect different situations to provide additional gameplay options to players (auto-detecting where possible 'watchtower' locations or 'wall' locations can be built, or where new towns can be founded, or where pathways should go, and by what routes rivers should flow).
Third, if I'm going to do hand-tweaking of the terrain post-generation, I'd want to build tools that allow you to rapidly make large-scale tweaks to allow content modification and construction to be as fast and easy (and still high quality) as possible. i.e. not placing each plant manually is a common tool feature.
