Matt,

your analogy sounds good but does not stand up.

Spam was never the the probelm with email and it is not with notifications. Gmail´'s tabbed interface hugely improved email, by automatically categorising items and hiding non urgent matters that could be looked at later
Right now we don´t even have an inbox for notifications. Developers put them wherever they feel like.

The WP Notify project seems like a workable the answer to me, what do you propose?