People expect machines they interact with to behave in some kind of logical manner. After 2 or 3 times of submitting an article that HN has traditionally liked -- and watching it tank -- just not that motivated to submit more. After submitting my own articles, having people stop me in the hall and tell me they liked it and voted up for it on HN, only to see it have no votes? Not so motivated to submit more. After the tenth conversation about how people expect HN to act one way and instead it acts another? Not so crazy about it.
I think the problem here is that PG wants folks to participate, but only to a certain extent. People want to interact with the system, but on some kind of mutually-fair terms. I'm not sure PG's goals line up with the average user any more. There are good reasons for this, and I'm not trying to trash the entire effort. It's just that this is a tough problem. I don't think you can code your way out of dealing with messy human issues at scale. If you could, we'd all be managed by computers in 50 years, and that's not a future I would wish for my children.
Short answer is HN is basically deal flow for YC. To that goal it obviously works very well.
PG and YC need "everybody" but yet they need "nobody".
As a business HN works to achieve the greater goals of YC. I don't think it is about anything else and I haven't been around long enough to know if things were ever different. They may have been back at the start because I guess if you were to arbitrary you would never build up an audience or fan base.
On a personal level I've always thought that people who get up to the karma level you are at actually deserve some special treatment because to me the top commenters are some of the glue that makes a place like HN special. In any business I have ever run you always give special treatment to the better customers.