The second big issue I see is when responding to comments on a post about you/your company. I'm at 950-ish, and I suspect that is on the high side for a founder at a 2 year old startup. When posts about us hit 3 months ago I didn't have 500 points. I "hustled" to get to this level so that I would not look like a noob, but if these rules had been in effect 3 months ago I wouldn't have seen comments and questions about our product, and I wouldn't have been able to reply.
I'm a "noob" as I have under 1000 points, but I have been a top 100 contributor in many other communities, it doesn't sound to me like this is a good idea. I think it will limit discussion and feed back by Authors, Founders, and others who find they are suddenly getting traffic from a site called ycombinator that they have never heard of.
Basically I think this is a move away from community and towards elitism. If that is the goal, then I think you should do it, but it feels like it is counter to the stated goals of this change.
@PG if you want an automated system for determining the quality of a comment I make one. We could probably work something out to leverage our technology at HN to prevent all the negativity, and to do some sort of blend of the quality score of the comment and the user karma to calculate if the comment "passes".
I posted a history of Digg and how changing the way powerusers and noobs were treated lead to its downfall.