The problem is that Rock has never been one thing - there have always been different varients running side by side.I think, as couple of posts have noted, you have to include the Velvet Underground who did, IMO, draw on a different tradition to mix with those that influenced The Beatles/Stones etc. In many ways their influence has been just as pervasive and, for me, is seen in much of the more interesting music of the past 40 years. I think the Banana record has been more influential than anything Hendrix recorded - much as I love Hendrix. Look at any ATP bill, for example.
So an alternative rock tradition may run something like -
Velvet Underground and Nico
Captain Beefheart - Trout Mask Replica
Patti Smith - Horses
PIL - Metal Box
Radiohead - Kid A
Still Rock with guitars, bass and drums, but using the rules in a different way.
Should we note that women don't figure much in many of these lists?
Kevin