I do see your point, though, wrt top users not spamming the site. That's largely why I liked your idea of throttling submission rates based on karma. New users should have to develop karma by being useful, rather than just prolific.
I know I suggested it, but throttling submission rates based on karma might not be fair to the end users. Once a karma-archy is established, the rich will get richer at the expense of the poor.
One solution to older users having a perpetual advantage would be to implement some sort of aging of karma, or at least of the karma value used to determine throttling. Such a thing would actually be a win in terms of SNR--it doesn't really matter how karmic someone was a year ago, if they have only made low-quality posts/comments in the past month, they should be treated (in the submission system) as a low-karma user.
The problems, of course, are that there is some fixed point, and also that news.yc may not fit the growth model that makes the above true for a community like Reddit--and that may be a good thing.
Points, or karma, could be rewarded based off a ratio of useful contribution to total contributions instead. Such a system would encourage a user to make sure his contributions to the community are good. This would be beneficial implemented in any crowd-generated news site.
While not another news aggregator, our project is addressing similar types of issues in other channels. I am loving the applied relevancy to here already.