I don't see what is bad about a system where you get better by doing, and get even better by special training. That's what this method is.
Not really, though. You don't get much better by doing, you are just enabled to pick perks by doing.
Frankly, I think the skill/perk relation is totally screwed up. You can become a master mage without any skillpoint or perk in the magic schools, all you need is enchanting to reduce magicka cost to 0. The weapon and armor skills are basically maxed out at skillevel 80; That's when you get the last +20% perk.
Because skillevel contributes so little, you don't have real sense of progression. You only get stronger by picking perks or getting new gear, and those give you such a high jump in power that you go from "I can't even scratch that guy" to "Well that was way too easy" in a single step.
Perks should be used as a bonus, not as the bread and butter. They should actually provide you with new abilites, like the zoom for bows and such, and not just add a flat bonus to your effectiveness. That is the job of the skilllevel.
Plus, perk trees should be real trees. There is no real choice involved once I decide to use a skill. That's why every Enchanter, Smith, One-Handed warrior, light armor user, etc is basically the same again. And because we lost some skills and so unspeakably many spells again, I feel there's actually a lot less replay value in Skyrim than in previous games.
/edit
Also, I find it quite sad that they could only make perks viable by removing the effectiveness of skills. Obviously they didn't come up with enough interesting perks to make them valuable on their own.