It's things like this that make me think that skills should have been categorized instead of grouped with physical attributes. Have survival, mechanical, physical branches of perks rather than the STR/PER, etc (ie Fallout's S.P.E.C.I.A.L.) attribute style. That ship has long sailed, I'm sure.
In order to maintain the current perk system, maybe consider some things are so generic they should be taken out as a perk at all?
For example, Cooking? Everyone needs to cook, people like to eat, right? Lock recipes behind perk books (IE. Cook Books) and collect them all to unlock the master chef perk that gives additional yield to cooking or something.