My only concern with the perk system is that we'll be able to choose a perk every single time we level, which I think is a bit OP. This was a problem in FO3 but FNV got it right by only allowing us to choose a perk every other level. Also, enemies need perks as well; the game would be too easy if no enemies had perks.
FNV did not get it right, 2 perks every level is one of the most popular mods for FNV. It was one of there worst design decisions. Like Todd said its fun getting a perk, it makes leveling up more fun. I think most players would want every level to matter, not every other. If this is that big of an issue to you and you really want SR just get a mod.
@Vtastek, good point. Getting a 1% increase in a skill is not very excited, I want to notice my increase in power, perks help achieve that goal.