The huge problem with email encryption right now is that you can't reasonably make it mandatory (as you can see, a lots of domain do not support it) so it can be easily be stripped à la sslstrip, and there is no such a thing as HSTS. (Again, please, build pinning into everything.)
So an active attacker able to MitM can simply turn encryption off, and those 99.9% make me wonder if that happened to the 0.1%...