1. Skill tree would be nice, but it wouldn't be the same as Fallout. (I could live with this change, though.) But to accurately model human learning, it must become harder to go back and learn/improve completely new simple skills when you get older, as well; something I've yet to see an MMORPG do.
2. There's no good way to do that. If by limited by people involved, that will lead to abuse by higher-level players. Plus there will be teammates/random passers-by who will want to jump in and help. On the flip side, if it's limited by area, random passers-by who DON'T want to be involved will be annoyed by the slow-down.
3. Yeah, I can't think of any way to explain a huge population in a sparse wasteland.