> There is no standard for encryption or any other information security mechanism.
I agree that SSL in transit and GPG could stand to be improved, but they do exist.
> No server identity verification.
What do you want that SPF+DKIM doesn't cover?
> No delivery confirmation.
Good? That sounds like asking for abuse. And in any event, it's no different than inline remote images (which of course are blocked for the same reason that delivery confirmation is a bad idea). Unless you just mean being sure that the message got to the target server, in which case I agree that the best we can do is delivering it directly to the target MX and see that it confirmed that it received the message.
> No push standard.
Temporarily true, pending JMAP (which I suppose strengthens your point about needing innovation).
> No concept of groups or other ways to categories and manage access between users in a domain.
Not quite sure what this means. Do you want something like shared mailboxes and tags?
> Every provider has their own implementation of threaded conversations.
True, though in a message-centric format I'm not sure that it's a bug.
> No major provider supports non-ASCII addresses.
Not a bug in email, only arbitrary restrictions by certain providers. Also opens you up to unicode normalization attacks (phishing is easier if you can fake characters).
> Servers can't even agree on simple message formatting.
I'm not sure what formatting servers even care about (email is just some blobs of text strung together), but I can't really refute this without knowing what you refer to more specifically.
> Most things that make email actually useful are outside the spec and tacked on by each individual provider.
Email is useful because it lets us send arbitrary stuff (usually a text body and zero or more attachments) between federated providers. It's a simple-ish protocol that is stable and just works.
EDIT: In summary, I vastly prefer email as it is: A simple protocol that can include arbitrary information, which allows people to extend it however they want. Of course, this means that extensions are arbitrary and at best non-required, but that keeps it flexible and back-compatible.