I would ask what the goals of the change are, but they seem obvious:
1) Limit nastiness and negativity
2) Encourage deeper and pensive comments
3) Cynically, it seems like a private goal would be to limit criticism of YC, though I know this would never be a stated goal. The criticism may simply have increased the priority even though HN has seemed more civil in recent months as an outside observer.
While the change may achieve these results, I would expect the following effects:
1) Fewer comments overall (there is a new "tax" to post, so-to-speak) and as a result there will be fewer visitors in the medium term (sites like HN, reddit, slashdot, huff post, etc all thrive on both the quality _and_ quantity of comments since that's what entertains people). Without controlling the number of front-page stories, you will in effect decrease the available content for viewers to consume. The demand will be filled elsewhere. I always assumed there was a private, invite-only forum for YC and that you would leave HN alone as a great PR platform... this move makes me wonder some more.
2) Comments will trend towards the quality of bane, tokenadult, ChuckMcM, patio11, cperciva, etc (we all know them) at the risk of fewer "provocative" posts. Often the greatest quality posts, however, are in response or to contradict simple-minded or provocative posts.
3) I am concerned by this line: People who regularly endorse comments that fail one or both of these tests will lose the ability to endorse comments. I like meta-moderation and all, but I don't like being reminded that all actions are recorded and tied back to my account. I would ask for some separation between "endorsing" and "agreeing" -- as a continual skeptic, I like reading and promoting contrarian views since it helps us learn.
I look forward to watching the experiment, and as a parting request, would you be able to record and measure the goals? There must be a YC company that can help with that, and I imagine it would be a wonderful blog write-up!
Which means such topics are dead to HN. What remains? Something we can't predict right now, but I suspect it won't be what we want.