Deeper richer story that is not so linear, or one tracked.
How is the NV story
linear and onetracked, exactly?
I can agree with having more depth and richness to it as more of them is rarely a bad thing even with already good stories, though I don't consider them as necessarily "needed" in this case.
------------------
On topic:
More skill/stat driven gameplay (skill/stat requirements for weapons that actually make a real difference, bigger effects on accuracy and recoil, for a couple of examples).
Different levelscaling scheme in the MQ areas and with weapons (more "step based"/"non-linear" levelscaling, higher level weapons available earlier on, but not easily, and with requirements that give a real punch).
Difficultyslider that does its job - and overall more challenging game.
Slower paced characterprogression (compared to the amount of stuff there is to do, I always felt I got too good too quickly - though that has also to do with the general level of difficulty).
Better balance with Factions and their quests (more equal amount of stuff to do with and for each).
(turnbased combat, map node system)