We are better than the Pebblesorters, because we care about sentient lives, and the Pebblesorters don't.
Translated:
Humans are preferable to Pebblesorters according to human utility function, because humans care about maximizing human utility function, and the Pebblesorters don't.
But that's not what "better" means at all, any more than "sorting pebbles into prime heaps" means "doing whatever pebblesorters care about".
There seems to be a widespread impression that the metaethics sequence was not very successful as an explanation of Eliezer Yudkowsky's views. It even says so on the wiki. And frankly, I'm puzzled by this... hence the "apparently" in this post's title. When I read the metaethics sequence, it seemed to make perfect sense to me. I can think of a couple things that may have made me different from the average OB/LW reader in this regard: