Nobody ever really argued perks were a "Naturalistic" way to enhance your abilities. But it's a way of making each level feel significant. It's definitely what made leveling in Fallout 3 and NV rewarding, as opposed to Oblivion and Morrowind where with each individual level it was just kinda pointless.
Oblivion in particular, Attributes felt very useless. If they are using Oblivion as the baseline right now, definitely removal was the way to go. I actually found attributes to be a bigger burden than asset. For one, they're hard capped at 100, except for Magicka, encumbrance and stamina(Fatigue) related calculations. Secondly, each level actually feels like an insult, because if you didn't score all 5x modifiers, you feel like you are going to be gimp now.
Morrowind on the other hand, Attributes were significant and, actually a little too easy to exploit. Super high agility made you entirely invulnerable to basic attacks, pounding a few dozen Sujammas made you, essentially Thor, god of Thunder, smiting foes with the might Hammer Mjolnir.
But it's kind of funny seeing people try to explain out the naturalistic failure of "perks" while at same time, praising attributes, when they essentially function exactly the same at best. It's semantics, nothing more.