+1 to balancing the skills via a penalty instead of a per/short rest limit.
Theoretically that would be good, but I don't have faith in Larian balancing abilities. It tricky to create drawback strong enough to not make the skill always desirable but mild enough to make the skill useless. Going for a simple enhancement but limited use is just... easier. 
I personally think they are not limited enough - I am unlikely to use them until I encounter tough fight, but if I do encounter tough fight I am likely to short rest after.