Perks are essentially percent boost and mainly that is it.
I liked the whole natural progression system they used in Skyrim. Made you work for the perks you wanted and provided incentive.
Other than that I don't feel perks to be an incentive. If I play any class, class based perks are needed (!) to actually make the accompanying skill usefull.
Ie If I wear light armor.. I need to invest in these perks to boost my DR
If I use one handed... I need to invest in one handed perks.. my "normal" skill boost will do next to nothing in my ability to cause damage... and so on and so on..

