Chomolungma said:
I'd say this should be a vote for the character you prefer, rather than the anime you like the most, although that's just my opinion.
True, but it's a poll already skewed by the fact that someone else shortlisted the characters in the animes anyway. I think it's more intelligent to "vote for the character in the anime which has your favorite character from each anime in the cast". Like voting for Danger Mouse because he's in the same series as Penfold, who you like more than Charlie Chalk (who you actually like more than Danger Mouse, but like less than Penfold).
^ The above paragraph is designed to disorientate people into voting exclusively for Char Aznable in every character battle he's in. And even a few he isn't in.
DaNiMé said:
U should just make the rule, you can only vote if you have seen both series'; that makes its perfectly fair... less votes, but fairer votes
It's essentially impossible to enforce, but a good idea nonetheless

What if there is some weird combo that comes up later, that no-one has actually seen? I suspect "Naruto Vs Tohru" wouldn't work to well

In all honesty, I can only vote on "Spike Vs Vash" and "Tohru Vs Osaka" by those rules. I've not watched 10 out of the 16 Shortlisted shows...
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A New point to make: it needs to be cleared up whether the "battles" are about which is your favorite character, or which "would win in a fight", because a number of people are interpreting it in the later way.