I think the current system with caps is okay.
There are caps regularly in certain shops.
Also you can trade items for other items, for instance ammo so you don't have to go mining regularly.
I would be much more interested in seeing different pricing based upon geographical location on top of pricing based upon the interest of the trader.
For instance uranium ore costs 125 in BH and BH caravans, but would cost 175 in NCR, 225 in Junktown, 250 in the Hub, 300 in Adytum, etc.
Towns like NCR with mines would have normal prices for anything craftable from normal minerals and ore, but higher prices for stuff made from hq ore and minerals.
Meat and hides would be cheaper in Modoc than everywhere else, hq and the stuff made from it would be cheaper in Gecko, BH and Redding, drugs and medical supplies would be cheaper in VC, etc.
Stuff like skins and scorpion tails could be the same price in all towns they're close too, but more in SF where they're further from.
Also as raiders mostly get stolen stuff, everything should be cheaper there.
All of this includes both buying and selling.
Downside is that I think this is hard to build in.