My expectation is that only large feed consumers (such as FriendFeed or Gnip) will fetch SUP. Smaller ones will probably use an intermediary service such as Gnip since they would only be interested in a small fraction of the updates.
They key purpose of SUP is to make it as easy as possible for feed publishers to let the world know which of their feeds have updated.
Say... first 100k feeds reference sup1.json, second 100k reference sup2.json, etc.
And given that each RSS/Atom feed <links> to its SUP feed, you could reorganize arbitrarily by updating the link, and the poller should pick it up on the next go-around.