Lists like these always cause controversy over the criteria, if this list is based purely on guitar SKILL, then of course there are some I disagree with, however most of them factor in originality, influence, song writing ability, etc.
Some of the guitarists near the top, George Harrison, Keith Richards and Kurt Cobain especially, no where near the skill level of some of the players near the bottom, but have written iconic songs for their generations and influenced many by their playing style.
The list is for "Greatest" Guitar players, not most technically skilled. JMO