I am not a big super fan of best guitarist lists as a rule, but Spin's is more focused on creative and influential sounds than how many notes somebody can play per second. Best guitarists lists usually remind me of self-proclaimed "music experts" in high school who said you "had to appreciate Rush, because they can play, man." I mean, if that's your criteria, wouldn't ANY CLASSICAL MUSIC be automatically better than rock because of all the training and competition the musicians have to go through? Yes, early 70s prog-rock values survived in my town way through the 80s. It doesn't matter how well the band members play if they don't do anything interesting with it.
My main criticisms would be that somebody is suffering from severe grunge nostalgia to put Pearl Jam on the list of anything great except for their amazing ability to convince people that imitating Bad Company was alternative in any way. Also, Kurt Cobain wrote some good songs, but I don't really find his playing that exciting. Some bands are more about the whole, like I love Guided By Voices, but I have trouble breaking them down into separate parts.
I suppose I'm dating myself as well with my additions, since I love the late-70s, early 80s guitar sounds where it's slashing and metallic, all shiny and full of glass shards, or creepy and ominous like a black helicopter landing. As post-punk comes around again, though, it can't be said to be uninfluential.
I would say the number one forgotten progentor of this sound would be Roxy Music's Phil Manzanera. Here he is at his most creepy:
And where would Stephen Malkmus be without Colin Newman and Bruce Gilbert of Wire?
My number-one underrated guitarist would be John McGeoch, maybe because he played in several bands (Magazine, Siouxsie and the Banshees, PIL, Generation X), so he didn't create an identity with the public. There'd be no Johnny Marr without him, though. This one always gives me goosebumps: