The perk system is better then Fallout because it requires you to become more specialized which is exactly what people complain about when saying they miss the attribute system. Basically they dont force you to roleplay a certain character based on invisible barriers. You are instead forced to specialize by using(or practicing) certain skills and then being able to unlock certain perks depending on your level in that area. So your role play has more freedom but still has to be specialized in order to beat the game on anything but easy, apprentice, or adept. So youd rather be "locked in" then have to freedom to roleplay in a more realistic way? The perk system IS tha attribute replacement. The reason lockpicking can level a mage is because it's the perks that determine the strength of your character not the level they are in certain places. The perks have a stronger effect on the game then almost anything else in character development.
In Fallout 3 and New Vegas perks were sectioned off by level, as well as potentially having both skill and attribute requirements. So not only did your character have to have certain skills, as well as attributes to match, but also had to reach certain levels. Granted, a high intelligence character got more skills and therfore more options, but that is still specializing the character, because it's a trade of attributes, potentially locking him out of certain perks. Sounds more specialized to me.
The Skyrim perk system could've been good, if it had been better implemented. Take a look at the one-handed tree, it's pretty much just damage increases. Perks doing what attributes used to do, in a fairly over the top way, rather than actually demonstrating higher levels of skill. A Fallout style system could've resulted in perks that required stats and skills, necessitating a greater level of specialisation, rather than a half-hearted attempt to compensate for the lack of stats.