But most of it makes sense, I mean if you don't understand that this entire area (which is quarantined off by a corporation with those massive turrets in the outskirts) has been dominated by the foundation and gangs. The gangs are mostly drifters who are just holed up in some camp, and they delivered that pretty well. The towns you go to have a population, but it would make sense if they're not out and about all the time.
After all, your team is rather unique, right? They're the only people besides the foundation and guardians looking for the vault.
All the other enemies in the game are animals, and they have a pretty good dwelling attitude in the game.
In any case, the game barely passes as an RPG. I think the mechanic is really only there because you pretty much have to have RPG elements in an open world game now. But, mostly, the levels only attributed to the skill points. Which is akin to something in an action game with upgradable abilities, just ... maybe it makes more sense to use experience points rather than enemies spewing bouncing orbs in addition to items.
As for the split between merchant vending machines and the people themselves ... the people run the vending machines, and they themselves are free to do other things. But it makes sense mechanically too, it makes it so, A) you don't have random merchants at the beginning of every dungeon and B) you don't have to get your quests and items from the same interface, which would probably be confusing.
Those terminals were there so the areas were separate maps ... they're pretty damn enormous, and without a live level streaming system (unreal engine 3, remember?) it's pretty mandatory to have load points. What's better with having the terminals is it actually fits with the world (as they're also your respawn points), not to mention they offer plenty of player convenience, like only loading a new area when you actively initiate it, not just when you hit some invisible barrier to the next area. They also act as teleporters to any other similar post you've encountered in the game, which is a godsend.