I don't know if this specific idea has been mentioned, I haven't seen it, but what about having a central perk tree, tied to all skills, that gave you ythings like running speed bonuses and encumberment bonuses and general damage bonuses and magic bonuses etc, basically what the perks do. Now, each skill will have a certain level of influence on some of the lines in this tree, and once you get enough skills that go under one branch, you gain access to the next perk in that branch.

I just realised that this is basically a less dynamic version of attributes, but there you go, how about that? Because you can't put things like running speed and strength under skills or the 3 stat meters.

I'm not sure because Pete said all attributes have been folded into perks and health/magicka/stamina.

It's an interesting idea. It's possible some strength perks could go under stamina though...