From what I've gathered, the reason the train does not go to Klamath or Modoc is because building a train in an unguarded town would be too risky. I guess this is what the caravans in most towns are supposed to be, but why not have NPCs in each town that will take you directly to some towns for a price? They could be a little slower than the train, but if players can have vehicles like hummers, why couldn't merchants and other people in the wasteland?
So, for example, from Klamath there's three NPCs who will take you to SF (300 caps), to Modoc (100 caps) and to VC (200 caps). (Prices and towns are all examples, but it seems like adding every single town to the lists would take a lot of work.)
They could even take you to and from semi-secure areas outside of towns (like train stations) that would have a few merchants, more "taxi" NPCs and a few guards (but not many so the danger of the north is maintained) or even have the caravan members themselves be the very weak guards.
From a realistic point of view, we can say that the groups of merchants in the north, unable to secure the towns themselves, have unified to give themselves secure places to trade, travel and rest.
Edit: Thinking about this more and noticing people complaining about the north being unsafe, this could finally bring life back to the towns. Instead of making the towns safe and giving PvP areas, make these places safe and the towns remain to be PvP. What remains in town could be important strategic things, like profession masters, quest NPCs and NPCs who sell things like detonators and uranium. When taking a town, the controlling faction can also control the mine if the town has one and set it to a) warn and then attack all but reigning faction members, b) attack only enemy factions c)allow free mining with hired NPCs as regular guards.
