The other thing that didn't hit me is that I enjoy commenting on things that are on the "new" page -many of those stories don't make it to the front page and as a result comments don't get replied to or upmodded as much.
Forget commenting on anything that won't hit the front page.
Also forget commenting later on in a story when it gets stale. Best to hit a hot story when it is fresh and a lot of other people will be piling on later.
That's the point, guys. If the karma/colored system didn't affect user behavior, it wouldn't be there
Another approach would be to normalize the comment's score against the other comments on that story, and use a threshold on that. If there were 4 comments with karmas 1 to 4 and another story with 100 comments from 1 to 100, the 4 on the first would be just as good as the 100 on the second. That might be too much work, though ;)
comment karma / min (1, max (story karma, 10)
But your normalization idea might work better.
It's much like startups. Many of them fail, but the ones that succeed tend to succeed big.