With all the standard caveats about personal opinion and the fact that these sort of lists inherently always have one sort of bias or another to them, a few gut-level reactions:
Jubei? Really? Blandy McBlanderstein? I mean, sure, Ninja Scroll was fun for what it was, but... Jubei?
I agree with Kaneda, but not necessarily for the reasons cited in the list. Sure, he's a pretty stock street punk, but it's not the toys or the clothes that make him awesome. It's that he's thrown into a situation none of his ilk could have imagined in a million years... and actually rises to meet it. Sometimes it's the common man who has to deal with uncommon circumstances that makes the best character.
Yeah, Naruto's too high, but given that the show that bears his name is still the closest thing the American anime industry has to a mainstream crossover hit right now, it's not like we couldn't have predicted it. Whatever. Just like Dragonball Z before it, it'll be years before anyone can look back at Naruto and judge it with anything like fairness. We're just too close to it right now: if you're not rating it too highly because you're a fan, you're rating it too low because of hype backlash. If anything, I'm surprised (and pleased) that they didn't manage to sneak a spot for Sasuke in there.