I feel exactly the opposite. Traditional, non-nested, forums with more than a few users end up with many pages of @author comments that make it difficult to track the course of the conversation. With nested comments I know exactly who someone is replying to and the topic they're discussing. I think the issues you're pointing out (top-level peanut gallery, no bumping, >24 hours old) are more problems with news-driven websites than nesting vs non-nesting. If you had a reddit-style nested private niche-topic forum the pace would be slower and the problems you point out would probably be less of an issue.
