1) giving E-Mails more inherent structure that is managed centrally (streams) instead of by each user (filters, folders).
2) making E-Mail more synchronous instead of asynchronous.
As far as I understand, you're arguing against (2). I agree with everything you wrote, however I still find (1) a very good idea. It is also an idea that IMO could be implemented entirely without changing the protocol - it's just a question of where you put this additional information. Streams could also simply be represented as a group address in the CC field that is managed differently by their client/server architecture, but otherwise fully downwards compatible.