Buckethead is amazing, and I don't think anyone here is stupid enough to dispute that fact. But, in my eyes, Paul Gilbert is a better shredder and all around guitar player, due to the fact that no matter what he plays, it ALWAYS sounds musically appealing, rather then just a mash-up of really fast notes, which is what I feel Buckethead sounds like sometimes.
I basically have the same point of view, but the way I see it is Buckethead is more at the extremes. He has a lot of really bad crap that is unlistenable, but the stuff that is good is AMAZING. He just has such a massive discography that it takes a long time to sift through the crap, but personally I think his best stuff far surpasses anything that the vast majority of guitar players have done. Gilbert is a great guitar player as well, and he actually taught buckethead for a year for anyone that doesn't know, which is why they sound so similar. A lot of Buckethead's music clearly has it's roots in Paul's style of play.
with guys at this level though it pretty much just comes down to preference, because they're all technically brilliant. I just pick up more emotion from Buckethead's playing which is what I look for in music.