Looking at the perks themselves, though... I actually think I
do enjoy the overlap between Perks and Skills: While in
Oblivion, it automatically gave you the ability to cast the next-tier spells, the perks seem to make it possible to just focus on mastering lower-level spells, which can be useful for Hybrid builds.
Same with the "Basic Utility Modifier" perks (Increased damage for all weapons of the type/Increased bonus from armor) - You can go for versatility, or absolute mastery of certain skills.
I love the flavor of the Magic School perks. The perk tree that seems to have been absolutely, thoroughly shafted though was Light Armor, because almost
all the perks require you to wear a full set. Hopefully, "Unarmored" counts as 0-point Light Armor.
... And the Speech tree really suffers from a case of WTF dependencies (You have to first be attractive to the opposite six before you can sell your loot?) ... I hope those are just misplaced.