> What about an alternate messaging system addressIng these issues ?

In case he was talking about unencrypted email, it's obvious:

-> Only use encrypted email (with an email client).

In case he was talking about encrypted email, all the "metadata" is still open (sender/receiver address, time/frequency, message subject). Then you can cross-reference that data with other data to get a more precise picture of the users.

-> Only communicate using one of the "darknet" platforms: https://en.wikipedia.org/wiki/Darknet_%28file_sharing%29