You can add layers to a protocol definition, but it's nearly impossible to "fix" a protocol.
Email is what it is, you've been able to layer on PGP encryption since its inception in 1991, but most people don't.
So generally it's better to start with a protocol that is built from scratch with the features you want.
I would definitely not change the smtp protocol. I would not even touch it. I would only make an app that makes it easy to encrypt.
But definitely easier if the protocol itself contains the security and privacy features you want.
But there is also the power of already established protocols, that many use.
Maybe the a good way is to somehow have both. Have a bridge, that gives easy access to the new thing via the old, so the transition can be seamless.
