@Ubiq:
As far as the absence of One Piece goes… well, I dunno there. I would say elitism or something, but how in the hell do you explain Naruto then? Maybe it just isn't Japanese enough for them.
There's been some theories on why the poll spread out like it did:
1. 60% of those polled are female, with 40% male. Even if Gundam Seed sucks arse, it's popular with boys because it's GUNDAM ('lol') and popular with girls for the bishounen.
2. Those polled are of an older demographic than that which OP normally caters to.
3. Recent shows tend to do better than older ones, except exceptionally memorable shows such as Evangelion.
So, by theory number one, Ichigo and Naruto's presence would be indicative of them having (arguably) more attractive designs to females than, say, Luffy or Goku.
Number two explains why odd characters like Mizuho or Shana got on the list; older male fans like traps and lolis and would vote for them.
The third follows what you outlined; newer shows like CG have a number of main characters in said poll.
There isn't any universal theory, but I think those three pretty much cover the output.
@Rixter:
It's just a goddamn list. About what some die-hard anime hippies think. So what?
And ratings are just arbitrary numbers that have no impact on where a show is broadcast, its censorship, quality, and frequency of airings. Sales, advertisements, and premise direction are totally not dependent on what people actually like.