It also allows client-independent strengthening of the hashes, so you don't have to wait for users to login again to be able to increase the strength of all existing hashes.
GP might be thinking of cases where the Nth iteration of the hash is only based on the salt and the result of the N-1st iteration, rather than on the original passphrase.
I'm not aware of any currently recommended algorithm that does this, though. The original passphrase usually goes into each and every iteration, not just the first round.
Exactly, it's hacky, but Scrypt'ing your ancient MD5 databases is better than sitting on your ass and being caught with your pants down when your database gets dumped on pastebin or a Russian forum