Why don't botnet operators use a peer-to-peer style command centers? According to the original article on the FireEye blog, the network was taken down with only "three days of effort."
Those might be vulnerable to anti-spam agencies actually hacking the control protocol. Or maybe it's just harder and the spammers don't want to spend as much time designing it. If government agencies keep taking these things down, and if they can do it quickly (not four years later), then it might be worthwhile for the spammers to have more robust control mechanisms.
Some of them do, notably Zeus. It takes quite a bit of work to make a botnet take instructions in a peer to peer fashion, so only the most sophisticated pieces of malware offer that feature.