This has been something that has bothered me for a while. Skill level contributes very little to your power, with perks having about 90% of all of the power in a skill. This means that skills have little use beyond meeting the skill level requirement for perks. Some skills are borderline useless without perks in them.
This is actually a good thing. Given that you have a limited number of perks, it avoids the Master of All that would otherwise happen by virtue of playing. Since you need perks to make skills as useful as they can be, and you don't get enough perks to fill all the skills, it encourages you to specialize if you want to get really good at something, or risk being merely adequate in a lot of things.
Being that a defining feature of TES games, ever since Daggerfall, is that you get better at what you do, having skill prerequisites for those perks keeps that alive. It's not simply XP -> Level Up -> Select Something To Improve (whether you've been using it or not). You have to use that skill to unlock the perk that can make the skill more useful.
- Smithing. The whole tree is borderline worthless if you don't have perks in it. You can have skill level 100 in it, but without perks all you can forge is bottom-tier gear. Perks should be nice little bonuses that are relevant to the skill, not as a requirement to actually use the skill properly. It seems like Bethesda implemented smithing, couldn't think of any good perks, and just put arbitrary restrictions on the skill that could only be undone by wasting a bunch of perk points.
You can still improve weapons and armor better with a higher skill, even if you don't take perks. You may not be able to craft them, but you can improve what you find (until you start getting enchanted stuff, anyway).
Where Smithing really fails is that there's so little to do with it. You create and/or upgrade your gear once, and that's it. Unless you grind the skill by creating and improving useless junk, there's no way to increase the skill more. If Bethesda had left in the armor/weapon degradation they had planned (that is, having your improvements wear off over time to bring it back to base stats; they said it was going to work that way before release, and I can't understand at all why they ditched it), it would have given you a reason to go back and improve your gear again for more skill points, without having to grind and without making it mandatory.
- Enchantment and Alchemy. All enchantments and potions are incredibly weak without perks.
These are still somewhat useful (alchemy less so at high levels, but not worthless at lower levels). A lot of the good enchantments you find are on otherwise low-quality junk, like hide bracers or leather boots. If you're wearing glass or dragonscale, then the enchantment skill lets you get some of those bonuses on your better gear, even if it may not be as good.
Ultimately, I think the idea with making perks so powerful is that it encourages specialization, without resorting to the old XP-based leveling system. For instance, you can't be a great mage and thief without sacrifice to some magic or stealth abilities (eg, sacrificing conjuration and alteration for sneak and alchemy). If the perks are too weak compared to the skill, then it's not really specialization more than simply minor, almost useless buffs to an already powerful skill.