See my post above but a whole new p2pool system would be neither desirable nor necessary. Currently p2pool doesn't have the hashpower to make more complex system necessary.
In time organically p2pool hashrate will rise and with it the difficulty. At that point a p2pool could be forked to have a longer share window. This would increase the difficulty even higher. That is all that is necessary to form a p2pool backbone.
If subpoools are ready to form & connect at this point smaller miners would simply create/join a subp2pool. Existing pools could already be part of backbone and would now just be operating at a higher difficulty level.
Rebuilding from scratch isn't a good idea.
Really to support a backbone & sub pool model only two things need to change:
1) The backbone p2pool needs a larger share window. This is because LP at the sub pool level will be based on LP both internally AND at the backbone. With 10 sec on the backbone and 10 sec locally that will make LP interval too small. This is a simple step (difficulty is simply increased by the multiple of window size) but shouldn't be done until sub p2pools are ready.
2) The current protocol is limited to 1 share = 1 address. However a sub-p2pool (or conventional pool wanted to provide transparency) would want 1 share split among multiple users. So the protocol would need to understand 1 share = n addresses. This change is latent so could happen at any time.