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To (a) and (b) I would also add (c): The signal to noise ratio goes down, so it's more difficult to find and upvote the best comments. Moreover, when there already are a lot of comments - and this can happen very fast - new comments, even very good ones, have a very difficult time emerging, and I guess this creates a disincentive.

One solution to try could be to give more time "up there" to comments from commenters with a high karma (only considering the karma from comments, not that from stories, which IMHO is a completely different signal).

I have noticed a bit that the top ranking comment will then contain a bunch of fragmented, semi-unrelated sub-conversations and the top comment almost becomes an OP of its own.

Yes, I noticed the same thing. Sometimes the first comments becomes so long, that it's almost impossible to reach the other comments - I even built a Chrome extension to be able to collapse them, but when the first comment is really too long it becomes difficult to manage anyway.

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