The original roleplaying game was of course Dungeons and Dragons. The creators developed the system they did by thinking about how they were describing themselves, and then using those words to create their own formal set of rules.
"How strong am I/this character that I control? How intelligent?" These are the things they asked themselves. Thus the rules, and consequently the stats such as "strength" were products of them placing themselves in that world. As well they were easy to understand for others. "Oh, I'm strong, so I should be able to hit things harder." It was a system that needed little explanation. Everyone already understood the basic concepts.
I think the way Skryim has gone has undermined this basic understanding, this ease of placing yourself in the world. No one has ever said "I have a perk." in real life; whereas everyone can at least understand the phrase "I am strong" and the implications therein. Rather than seeking to place the player in the world it seems the thought pattern went more along the lines of "what can we do to make this system of interlocking numbers more interesting" rather than "how can we place the player in this world."
This also goes with skills. Players like it when a skill seems to correlate with how they would describe that same skill to someone else in real life. "I'm good at sneaking around" "I'm good with a dagger." E.G. People in the real world would more likely say "I'm skilled with a longsword" or "I'm skilled with a knife." People naturally understand what this means. There was never any need to consolidate "Long Blade" and "Short Blade" into "Blade" because no one was ever confused by that. The perceived removal of complication was entirely unneeded.
This, I believe, is what has resulted in a lot of the complaints. And there are a lot of them, every discussion I have come across, on over a dozen different websites, generally seems confused or unimpressed with the reduction of skills and adding of perks. It's taken away the intuitive understanding of things and replaced it with unnatural rules. Rules that are in some ways simpler true, but a simpler yet more artificial rule set is still harder for people to understand; than a complex ruleset of terms they feel comfortable with. You can describe a perk as "you will now deal more damage by sneak attack" but people will ask the natural question of "How" and "why"? Whereas is you tell them "you are now stronger" they will automatically connect that with "Now I can hit things harder."
E.G. A player wants to get better with the longsword. They use it, they see themselves getting better in the game. They don't have to think about stats, or choices, they're drawn into the game because it's a natural progression from doing something repeatedly to getting better at it. But then we introduce optional perks. This doesn't happen in real life. Suddenly not only is the player forced out of the experience and into "the game" of it all, but now they do have to think about things. They have to think about "if I get this one, then I'll be passing up all these other ones, and how will that affect me overall?"
Please note, this has nothing to do with the new "no classes" thing