While SMTP and POP protocols can be transmitted over TLS between hosts, which prevents reading messages along the wire, the email data itself is _not_ encrypted. A compromised SMTP server can easily read and copy any message received or transmitted.
And, even if you use a side-channel to distribute keys between the sender and receiver (to encrypt the data safely), the header absolutely has to be plain-text. Governments and companies scraping email meta-data is already a huge problem.
A protocol closer to Tor would make for much more secure email distribution, but it would also require a complete protocol rewrite. Potential death of email from a back-end point of view at least.