My first instinct on reading this question was like George's: "great, another one-site proposal from someone who's never heard of Yahoo! Answers." Now that I've read through the proposal, though, I kind of like it, even though it's far from perfect.
This hypothetical SE 3.0 actually isn't that different than SE 2.0. There are two major changes here that I can see. The first is the universal tagging system, which has obvious flaws but I think merits further thought. I particularly like how it's intended to act more like the labels used by GMail than the folders used by file systems.
The second major change is the centralized interface. That one, I think, could be implemented with less disruption to SE 2.0, would be helpful right off the bat and could be a good barometer for whether it's worth going down the road proposed by the OP. stackexchange.com already displays a list of hot questions from across the network, and I think expansion/customization of that list into a more general portal page could be really helpful.
stackexchange.com already knows who users are, because they're logged in. How about showing a customized question list there for each user? Users could choose to ignore questions from some sites altogether, and maybe choose some favorite sites to get a higher percentage of questions from that site. Just as importantly, the user's personal "interesting" and "ignored" tags from the specific sites could be taken into account.
mockup coming eventually
mockupbetter mockup possibly coming eventually but don't hold your breath
