These are all great suggestions.
If the On-site-notifications plugin is to be added to the core, I think it would be wiser to have an option to disable email notifications on the user end, and receive on-site notifications only, instead of 'Admin can disable mailing for a user' as suggested.
If we had more developers in the community this would be easier to accomplish, by dividing the amount of work trough multiple developers, and then Scott would review the code pushes. Relieving him from a little bit of the stress.
But with everybody's day job this can be a bit overwhelming, to even start pulling from one end of the knot in our sacred free time.
In regards to the more modern looking theme. I've started working on a new free theme, but it's gonna take some time. And eventually I'll be asking for some feedback from the community for a few design ideas I have in mind, once I start developing the question lists etc, so we all together can come up with a design structure that pleases everybody.
I've only been working on the Top Bar so far: