I love how you increase your skills through use in Elder Scrolls (especially Skyrim, which didn't have that broken attribute leveling system), but I'd prefer Fallout sticks to using XP for leveling. And I don't think they'll change that. I would like to see many, many more perks that let you carve out a playstyle far better than what attributes and skills can do. And I wouldn't mind them getting rid of skills and just having SPECIAL and perks, honestly, if they balanced it right and didn't remove any actual playstyles (you don't need to have a "Lockpicking" skill on your character sheet to be able to pick locks, necessarily, and perks can define your abilities in a different way).
At any rate, I want them to balance the progression around getting a perk every level. Getting a perk only every few levels makes leveling feel lopsided and less fun, and it's not like they can't balance the game around the character having 30 perks total instead of 15 or whatever.
If they do include some form of "skills improve with use", it'd be cool if we could get better with a specific weapon the more we use it. Like, when we pick up a Gatling Laser for the first time it's way less accurate and its condition decays faster on account of our lack of experience operating the thing, but the longer we use it the more we master it. Would also help make typically weaker weapons more viable in the late-game; I hate when my favorite gun or outfit becomes so outclassed that it's no longer even viable in the late game.
More "challenge" perks like Day Tripper or Lord Death would be fine, too.