What evidence do you have that, outside of perks, the entire leveling system isn't going to be reduced to something as scant as the ability to cast higher level spells, with no other benefits at all that are not costly perks?
I'm pretty sure that outside of perks, the skill itself does barelly nothing. Meaning that the skill itself main effect is to unlock perks.
And it won't be a bad game because of it. Sure, it means you cannot do all the builds you want and have something functonnal, like you cannot max efficiency on 17 out of 18 perks and feel different from your last run where you maxed a different set of 17 skills out of 18.
But the truth is, it's not the ability to max everything that allows you to experience all the game in a single char. In fact, the game experience is defined more by what you cannot do when you play the game than by what you can do.
You mastered the two handed weapon skill and finished the fighter's guild questline. Then you decide you want on the same char to become a master mage. Well, your two handed weapon skill is still here and all the achievements you done you cannot redo them from that new perspective. So in a sence, you just grinded those magic skills for completion sake and they don't really allow you to experience the world through them without starting from scratch.