I don't know that this social problem has a technical solution, but you're right that the "points" system encourages shallow comments. Unfortunately some people will always see a number as a score, and start gaming the system to increase it.

The problem with many submissions recently has been they are taken directly from reddit, and have content that sits well with reddit but not HN. The "Programming prodigy passes away at 16" story is a good example: it's tragic news, but the fact that someone has died is not necessarily a good HN submission. Although much of the discussion about Erlang and Haskell went right over my head, I think this site did better when those stories were oft-submitted, if only because it tends to push away the people who would prefer fluffy "human interest" stories. I personally have no intention of creating a startup but find pointers to useful technical ideas and tools here - more of those, please

So I think we need to concentrate on the submissions, removing stories of marginal interest to hackers, and being diligent in upvoting good stories and comments, and downvoting crufty comments.