If Bethesda learns from Obsidians writing and quest design in New Vegas, then Bethesda is taking a step into the right direction, the direction they used to be going until a certain game.
I agree with you completely - After playing MW, OB, then FO3 and FONV, then OB again I noticed that the quests in FONV are much more versatile than any of the other games. An impressive amount of the quests had multiple endings, and many of which also mattered for the game world. It felt like your actions actually had influence.
TES games already have perks in them. you get perks everytime you become a journeyman, expert, or master at a skill. its exactly the same thing.
This.
Plus, you get them as quest rewards sometimes. For example after helping the Gray Prince your blade and block(?) skills are permanently increased by 2 or something. That could go as a 'perk' somewhat, too.
Last but not least, I do love crippling enemies and I think that location based damage as handled in Fallout would be great to see in TES too:
If I'm an archer, I want to be able to render my target immobile by shooting its knees, legs or wings. Dismemberment would be a bit too much (except for axes, maybe), but crippling is a must.