If CoD can do it Skyrim could.
That's actually the first thing people cite as reasons not to implement locational damage. TES isn't CoD. A lot of people are of the mindset that the
player's skill should never be as important as the
character's skill. Locational damage elevates the player skill past the character skill, so someone with no skill at all in Archery can still one hit kill a boss because the player is skilled enough to land a headshot. Overall, I'm inclined to agree with that being a bad idea.
However, there are ways to tweak the system to allow for both, and that's largely to make the character skill do more than just determine damage. If it controlled speed (of either swings or drawing the bow), range of magic or archery attacks, damage, spell cost (that it already does, though it doesn't boost damage

), chance of getting a critical hit, and more, then I think we could probably implement locational damage more effectively. It'd be great if such a system allowed for non-lethal takedowns.
I do agree that magic should get a sneak attack bonus. Maybe connect it with the Archery-Sneak perk?