High and low shots are in fact easier to do with d20 than with 3d6. Just roll 1d10 (low) or 1d10+10 (high). The point is that an unlinear progression of numbers does not guarantee that contiguous hit locations will be contiguous on the table. And please do not repeat "it's all done there". I know it is there. The point is that d20 allows you to easily design more monsters, the ones not yet invented. 3d6 does not.
As for the likeliness of head shots, with the missile hit loc table, it is one head shot in 20 versus one body shot in three. Seems fair enough to me.
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