Length doesn't make an anime great, though. It's their popularity that allows their authors to keep them running so long. I commend Oda and Kishimoto for having so much creativity to keep OP and Naruto running for as long as they have (Oda, especially), but writers like Anno and Watanabe have managed to accomplish so much more with much shorter works (Evangelion and Bebop, respectively, both of which are arguably more famous than any of the major shōnen anime).
And trust me, no matter what he might've ASKED people to base their vote on, bias is inevitable. If people were really listening to him, every single vote so far would've been for Bebop (mainly cause all its biggest rivals aren't even on the list).
You know, Cowboy Bebop didn't appeal to me as much as others have. It was a neat story. It's simple but yet complex because of their complicated back stories. Spike did have an awesome "death" too.
Now Evangelion, that is some crazy shit. It did have a big impact on the anime society when it was introduced, and it was very popular. So popular they remade the series again. It's just the ending for the anime was so bizarre, it turned me off. As a mecha series goes, it is one of the more popular ones with a great story, BUT is isn't the most well known. That goes to Gundam Wing or Voltron.
Both had such a huge impact and influenced many. Gundam Wing became so popular, there were at least half a dozen spin offs with the same theme. I think Voltron(next to Power Rangers) is one of the most known giant robot animes where 5 people fuse together and create a bigger robot.
Do you see a bit of what i mean by Greatest vs Popular. Popular is a sub set of greatest. It is part of the total package as to what makes something great. The length is also part of it which helps a series become popular and it influences other mangaka to create series based on a simple idea. Some other things would be what that specific anime/manga has achieved, or milestones. Like DB and OP are known for how many volumes they have sold world wide. Pokemon is known for its awesome games. Yu Gi Oh is known for its card game, but may not have existed if Pokemon didn't come along first. Digimon was also heavily influenced by Pokemon as well.
I just keep going off on tangents....
There is so much behind the word greatness that "my favorite" or "popular" can't even begin to describe.
I'm curious though, Have you ever watched Watanabe's other great work Samurai Champloo? It is one of my other favorites. If you haven't do it!