Perhaps it would be cool to have render passes integrated in the scene structure. Is this possible?
it probably is possible but i don't see the advantage.
i suppose what you want is have render passes attached to certain places in the scene so those elements are rendered in a different way. well, currently you have scene elements attached to certain render passes for the same reason. 
It does make more conceptual sense the other way round though 
i think this is something that can change after the 1.0 release, when we can make bigger structural changes. one thing we might do is to make jme more shader friendly with support for techniques and passes on a material level like the stuff you talk about…
I envisage that the propsed render pass structure by Patmania would solve the Bloom overlapping problem of nodes when not using the current scene.
unfortunately it wouldnt since the stuff to bloom is drawn to another buffer(which has an empty zbuffer).