Now hear me out before shooting the whole idea down.
Here's what I suggest;
You could see other players/npcs/caravans/etc. on the world map as nodes. Small round "static" circles, like the junkyard for example, but the green ring moves based on the owner of that node. (Player moves, so does the node)
Each player would "carry" one node with him. (Even if people are following, this would just increase the visible power of the encounter)
All of the nodes are invisible until the owner of a node (party leader) does a succesfull perception/intelligence/outdoorsman check; the check takes into account both node's owner's SPECIAL and skills. Sneak could be used as a "defensive" skill, to make your node less visible to other players/npcs.
Only nodes inside the scouting area (Scout perk increases area by 1) can be seen (they still need the special/skill check tho).
Vehicles would make you hard to spot but would also negate all skill bonuses. Also someone on foot can't catch someone driving a car but if someone is stupid/clever enough to ram into a player with a car the car is taken with him into the encounter.
If an npc sees an enemy node it will perform an action based on the simple AI rules; merchant parties wont attack deathclaws and will try to run away (move away from the node) but NCR army will attack them (head straight on to the deathclaw node).
Whenever two nodes collide on the world map and one of the node's owner sees the other node both parties enter an encounter (Same as random encounters now, but populated by the nodes owner parties).
Each node has a dynamic stat, Power set to them. Whenever someone spots another node they will do a per/int/outdoors check and decide a power value for the node. When a player hovers over the node on the map he'll see tooltip/message that is the same as succesfull outdoorsman check on random encounter atm.
There would be no random encounters (except special ones I suppose) in the game what so ever anymore. With this system npcs would multiply in the nodes and if the node size is too large (5+ molerats for example) Another node/group is created.
NPCs such as a molerat need to eat something so I assume they would try to find ants and eat them.
There would be some seed zones that would always have a few "hidden" NPCs available so they won't totally run out. Also different types of NPCs tend to stay in their own location unless they run out of food.
Whenever a caravan leaves a town he'll purchase some equipment from the shops and take off. Players could enter the caravan nodes and hitch a ride or raid them. Whenever a player is inside an encounter it stops on the map.
When a caravan reaches it's destination he'll sell off the items.
Basicly this will just shift items back and forth from town to town. The more items/cash the caravan has the more power it has. Although sometimes caravans won't leave if they're underpowered (no slaves/mercs in town) or no friendly towns are nearby.
If a caravan is running low on power it'll replenish it by purchasing mercs. (Removing money & items from caravan and turning them into slaves/mercs based on the town the caravan is in)
Here's an example:
Lets say NCR army (Power 8, 8 people) is in zone 31,29. NCR party leader has high perception and outdoorsman and has the Scout perk (would be useful and not just some shitty perk nobody wants).
There is a Marauder party (Power 3, 3 people) is in zone 32,29.
NCR party leader does a succesfull skill check and spots the marauder node.
NCR party starts to move towards the marauders.
NCR party encounters marauders and as there are no players involved the server does a quick combat calculation and decides on the outcome. (This will reduce server load but still make the world seem dynamic, which it would be with this system)
NCR party has power 8 and all 8 are wearing "high end" gear. Clearly they win.
Marauder party dissappears and NCR party continues with power 7 (one of them was critically shot in the eyes and his head exploded
Example of what player might see when hovering a node.
And here's a mockup of a large area if you could see everything in the map. Nodes are colored different to differentiate NPCs/players. In game they could all be same color since you could easily just mouse over them to see what there is.