Discovery - can be built on what we have
Privacy - IP privacy is done by lower layers. If not good enough, fix it down there not up here.
Lack of data control - would a REMOVE command help? At the tooling level I agree, we don't have good tools, but at the protocol level what is needed specifically?
Spam - I think client-side we are in a pretty good position. Relay-side it is always going to be a nightmare IMHO.
Filtering - I think you refer to spam again, but if you refer to REQ filters, I think a (positive, negative, limit) system is better (probably off topic)
Email became centralized because it is a push-based system. If your sending server isn't "trusted" and might be a "spammer" then the other systems refuse to accept email from you. But the outbox model is a pull-based system (like websites are). You can always come to my outbox and see my stuff, nobody can get in the way of that. So I do not think the same fate awaits us.
I'm very interested in understanding the flaws and how it can be made better.