I am not sure I understand. You can rename caps to anything you want, but if you want to change the whole currency system it is not impossible with some work.
I don't think you can change the whole default barter system but you can use bobbypins or any item as a currency if you just remove all caps in game and add enough bobbypins in the world to have them in your inventory and remove all caps in the merchant's inventory to replace them with a levelled amount of bobbypins to use them as a trade currency.
Then you have no caps at all and you can only trade, Basically buying or selling is trading caps for items, here you trade bobbypins for items.
You can also use something like the machine in DLC dead Money. It uses casino chips but you can modifuy the menu to change caps to any legal currency you like.
You can even change the quest rewards and replace caps for bobby pins if you really want to get rid of all caps in game. eg : when someone sells some information for 100 caps it is very easy to change caps for bobbypins, but the only prolem is the dialogues will still say "caps". And changing all dialogues would be hard.
edit : I really need a new keyboard with all keys working.. Sorry for the typos