This far late into the game tells me notification overhaul won't be ready for iOS5. Being half a year away, I would assume that the feature list is pretty much set in stone by now.
Most likely, but:
Also, it would require some deep reworking of the plumbing for all apps, external and internal, to be reworked 100%.
I'm not sure I agree with this. AFAICT, all that really needs to happen is for alerts that are currently modal, instead be redirected to an onscreen message queue. The app wouldn't even need to know. I see this as a change at the presentation layer, not the messaging layer.