I didn't start out liking the system "in theory" but after playing to level 32 I've found it to work fairly well. I actually have a couple extra perk points I can't decide which perk to put them into, being I found out early that you don't really need scrounger, scrapper, or any of those type of perks so I re-rolled without specializing in them and only have to buy extra shotgun ammo which is easy with all the weapon vendors at the various settlements. I wouldn't like it nearly as much if it wasn't for the mountains of purified water I basically use like currency to barter for junk though.

I believe an overhaul mod (FOOK-like or something) will address these issues one day.