I agree with a solid Nope on Idea 1 except for one condition:
If you level up Mining you loose a bit in Farming
if you level up Runner you lose some points in Strongman
so on and so forth.
Lets people "specialize" in a particular area but not letting them "max all your skills"
Yeah, I was thinking a limit of 3 "extra" skills (from a large list of like 25 - Fallout type perks). Each skill has a disadvantage to compliment. Completely agree we don't need 24x7 players becoming Gods. Perks should only enhance how people choose to play (hunter, gatherer, warrior, scavenger).