Commentary I've looked at today suggests that JI is more independent than dependent. More details at:
http://counterterror.typepad.com/
I have a hard time believing many of these groups are completely independent at this point. While orders might not come from a centralized source to every operative, they are working together. The Bali bombings were similar to London in their design, and simplicity. They are proving they don't need planes to cause a lot of havoc.
JI likes to target Australians. "Gadahn" mentioned Melbourne (Aus), and Los Angeles (U.S) with his recent video. Perhaps what we saw in Bali was the 'Melbourne operation,' or part of it.
So many leads, so little concrete information... :-/