You see, The Elder Scrolls has generally been about emergent player choices, at least since Morrowind. Many players will start out playing as some sort of role (say, stealthy bow user), only to find that they prefer something else later (say, finding out they do better with a one-hander and shield and restoration magic). This would generally be fine, even with the odd way in which games like Oblivion leveled, but not anymore in Skyrim, because Skyrim functionally ties your powers to your perks.
Perks are generally far more powerful than getting skill levels in this game. In fact, skill levels almost seem to exist only to give us access to more perks, where the perks so overshadow what little benefit the skills themselves give that they hardly matter.
Now then, yes, this does force a player to choose whether they want to have one playstyle or another rather effectively, but at the same time, I have to ask if this is what we really even want? After all, this would mean that a player could train their one-handed skill up to a high level, then, work on two-handed weapons, and wield those for a far longer time, and bring that two-hander up to maximum skill level. However, because the player was only using the two-hander to gain skill ranks for levels, and put all his/her perks into one-handers, and the one-handers which you spent less time training would be more powerful than the two-handers.
What if the player decided he/she liked two-handers better? Without a perk reallocation, you're basically just stuck. You either stick with one-handers, or you have wasted a large number of perks, and are never going to get that power that would make other skills far more useful back.
Then there are the pre-requisite perks that make little sense and force players to buy things they don't want or need to get to the things they do want. Yes, sure, some perks are very powerful, but if I don't want to play a necromancer because of RP reasons, why do I have to take necromancy and dark souls to get my double atronach summon? Why do I need to take a perk that increases the potency of poison in order to get the perk which lets me gather more herbs? What do those two perks have to do with one another?
Wasn't the whole point of this system from the start that training and use = power? Doesn't this contradict the entire basis upon which the skill system that makes this game unique was built upon? This is an unholy matrimony of experience-point-based leveling with character points that I spend to min-max my character with the natural use and skill level system.
There are even solutions that involve keeping perks in general, but removing them from character level, and tying them, instead to skill level - so that, like with Oblivion, you could hit rank 50 in a skill, but then have a choice as to what skill you want to gain when you hit that skill rank milestone. Then, you can choose specializations still, but have it remain tied to your skill ranks, not your character level. Even more, you could require training to learn those perks, allowing for more immersion.