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The Atari bloke's native language isn't English so he doesn't always seem to make him self clear and probably misunderstands things sometimes, but he means well.
Regarding the comment system:
It would be nice if everybody could see the scores applied.
I don't think posts with negative scores should be "hidden", because people will still want to see what was so bad about it. I even tend to upvote them just because they're negative.
It's not uncommon to see silly, worthless or even plain inaccurate comments to be voted up and accurate ones voted down.
Why not keep it simple and offer two choices: I agree and I don't agree. And then display both scores. So a comment can have 4 agrees and 3 disagrees. Right now such a person would have a score of 1, which leads to believe nobody voted.
Why be able to mark stuff as spam? I rarely see any. OSNews staff can just remove them when they spot them. Also I don't see why you need to choose a reason to vote someone up if no one can see that reason.
That's also a good idea.
Though trolling is not easy to prove/judge often and flaming should be allowed if it's not just plain insulting.