To have an affiliate program at the network level, so that someone who joins the network can get a commission on referring other people to join the network and get their own member site. (Thinking Pro Sites here) (Maybe Pro Sites should have its own internal affiliate program)
And an affiliate program at the member site level so that member sites can have their own affiliate program and their members can earn commissions by referring others to join that member sites membership program. (Thinking Marketpress / Membership / Protected Content/ etc.)
Currently with the Affiliate plugin you can only do one or the other.