Bartering. Bottle caps are fun but not only extremely limiting, they don't make sense as a common currency. Not saying do away with caps, but the original game let you do the obvious thing and trade items with NPCs, not just merchants. I'd have a reason to pick up a lot of crap, and get items off locals rather than bringing a haul to a merchant like they're a Coinstar machine. This is one of the dumbest, least fun things ever, and I can't explain why the series was made dumber to be this way.
Well, so I hear the game will use the Skyrim engine, so my hope for better physics, animation, pathing, etc. might be for not. Creepy wooden NPC puppets that get stuck, disappear and general awkwardness may be here to stay.
More guaranteed perks through quests, and maybe rebalance and give a perk every level. Way too many to choose and kind of locks you into character builds.
Make reputation of factions easier to understand, manage and change, and deepen advantages/disadvantages of having or losing rep.
Bounties, including your own. Notoriety for anything you do and depending on your outfit. Factions, locals, law people should all offer bounties or have reasons to come jail or kill you. There should be some kind of law system if you're caught stealing or shoot someone rather than ruining your save file.