That sounds like an incorrect fix. Since the comments are separated by trees, they should be positioned and compared to comments relative to that tree, not relative to the master tree. Being at the bottom of a sub-tree marks the comment automatically as the most downvoted in that tree.
Applying fading to all the comments just because a downvoted comment has a parent that happens to be at the top, seems wrong.
Agreed. If they're this adamant about keeping the fading functionality tied to downvoting, they should just do away with downvoting all together, because fading just seems to worsen the discussion.
I've lost count of how many times I've seen perfectly good insightful comments around here that get ignored because some people decided to downvote them for some arbitrary reason. In fact, it's so bad, that I'd say I've barely seen any good instances of fading for the past year; they just seems to encourage group-think almost every time.
I'm ok with the idea of downvoting meaning disagreement, since that's how voting systems always end up being used anyway (not to mention pg approves of that interpretation as well), but penalizing comments to become practically non-existent based on a few downvotes (last time I noticed, a score of -1 started the fading) is just not conducive to interesting discussion.
Comments that most deserve to be downvoted (trolling, incivility, lies, etc) are inevitably going to garner a lot of downvotes anyway. It's only the ones which oscillate between one or two downvotes and upvotes in what may be controversial threads which most fall prey to what I consider to be the more petty examples of downvoting. The first couple of downvotes are the least meaningful, I think.
So perhaps a margin of, say, five or six downvotes should be necessary before any visual effect takes place. Not only would this no longer bias readers against a comment before having read it, but it would guarantee that the faded comments more accurately reflect the standards of the community as a whole.
Downvoting and threaded view is hard to combine. What you describe is the trivial way. It has the downside that if a comment has few subcomments, downvoting them don't accomplish very much.
Applying fading to all the comments just because a downvoted comment has a parent that happens to be at the top, seems wrong.