The perks will be directly linked to the skill your using. Classes are choices made before you even start the game. Not the same thing choice wise.
It's still a choice either way, who knows what the perk trees will look like, we might not fill up every single perk in a perk tree to get to the last tier of perks. I still see choices.
Hell, maybe I'm wrong and I'll miss the class function, but I think perks (and I know you'll disagree) will fill in the gap of classes quite nicely without the need of numbers.
Again, it's all a matter of preferences, some like numbers and rely on them, while others rely on visual representation to show growth/change. One side is not smarter than the other, it's just a matter of preference.