Skyrim is supposed to be about freedom.
Is having to invest a certain amount of perk points into a specific tree before you're able to get the perk you really want freedom? No, not even in the vaguest sense of the word.
Is having to commit to a build you've been building for most of the game because you simply cannot accrue enough perk points to make another viable freedom? No, not even in the vaguest sense of the word.
Is having to live with the fact that the higher level perk you recently "learned" rendered the perks below it useless (read: fact) or a complete waste of time freedom? No, not even in the vaguest sense of the word.
Those are facts. The perk system is bad. It does not do what it was designed to do (if it was even designed to do what we were told it was designed to do), and that makes it a bad system. You can like it, sure, but you honestly cannot argue that we're better off with it than the system that has worked perfectly fine for the longest time. There were a few quirks, but Bethesda could have fixed them and polished it a bit more before throwing it out the window.
In Oblivion, I could spend most of the game as a warrior. A beastly warrior that is unrivaled in strength and.. beastness. Of course, I can do the same in Skyrim.
However, what I cannot do is decide that I want to instead be a mage that's just as beastly. In Oblivion, all I would have to do is level the skills associated with spell casting and I'd be set. Yeah, that does little more than turn you into a mediocre spell-slinger in Skyrim. The real power behind the archetypes, and hybrids of them, are the perks that support them. Skills don't do nearly as much as they used to, so I'd be forced to settle with my previous build or a new one that would never, ever, everwork as a viable, standalone build, and all because I don't have enough perks.
Again, that is a bad system.
You think that if you use the term freedom you'll sound like you have a principled idea. You don't. Characters are free to build up as much, or as little, of any skill tree that they want. If I give you $100, what you spend it on is up to you. The fact that it's not $4,000,000,000,000 so you can't buy everything you would ever want doesn't change that fact.
I'm L39 with 10 perks in the bank. Why? Because I'm focused on what I'm doing. I'm not trying to master smithing AND master enchanting AND master 1-hand AND master light armor AND master destruction AND master restoration AND master alteration AND master sneak AND master archery. I have 1 point in sneak. One. I have 8 pts in Destruction. I have 6 pts in Restoration. I have 6 pts in Enhanting. I have 6 pts in Archery. I don't waste my perks. I don't put points into perks willy-nilly and then realize 10 levels later that I didn't care about that skill. If I decide to branch out into something else later, I can. I'll probably do another play-through after this game (first time I'm doing this in a TES game) to do a warrior type and do heavy armor, 1- or 2-handed weapons, and smithing. My characters have definition. And I'm free to define how they are. The scarcity of the perks give them value and meaning.
The OP of the original thread didn't like the perks because he thought that they could be more interesting. Say you could have an orc-slayer perk which gave you 15% bonus in killing orcs or an arcane researcher perk which gave you 15% bonus in finding spell tomes or whatever. And that's fair. There could be more done with the system. It could be made even better. But even as it is right now it's already better than what did exist in the previous games.