My two cents is that, by having your skills balance themselves as far as level progression instead of major/minor skills, it makes it a bit more organic and balanced overall. By replacing attributes with perks and HP/MP/SP progression, you get not only more character-specific improvements from the perks, but more direct improvements on the general scale (instead of leveling endurance to raise HP, you just raise HP).
So all in all I think this system looks very good.
So what determines how much you carry? A perk?
What determines how fast you run? Perk?
How high you jump? Perk? (keeping in mind there is no longer a skill related to this)
What about how fast you regenerate magic? More perks?
How about how personable you are? Perk?
It doesnt really seem like a refined system. It seems like removing something so that a perk can take its place. That to me anyway, is simplified in a bad way. Instead of progressing your warrior's strength or your mage's intelligence (magic based) you simply smack a perk on there and call it a day. There was a whole system of progression that was completely removed, and now a miraculous 'perk' determines these things.
I guess its just a miracle every time you level. Something weird changes inside of you and you magically (only magic isnt involved) learn a new skill, or power, or improve an existing one. It all seems kind of childish and silly to me.