Envoy Cruisers have diplomatic immunity during their normal travels between embassies and cannot be attacked.
Like the others, I also hope there's a way for Envoy Cruisers to be attacked. NOT a way to suddenly get hostile on a single empire's envoys, I mean a sort of declared "Closed Borders" option where you flat out refuse to give diplomatic immunity to any other empires; diplomats don't get immunity just because they're diplomats, they're immune because the country they're going TO has agreed to give them immunity beforehand (revokable only by Danny Glover).
The downside would be that your friends wouldn't be able to send their own envoys for legitimate purposes, and you wouldn't be able to send out envoys of your own. But when I'm in flat-out war mode, with every other empire hostile, I should be able to reject ANY of their ships in my borders, because in that situation, I have no reason to give immunity to an enemy nation's personnel.
What I really want is just a bit more complexity. I want propaganda missions, to change the threshold where the other faction capitulates (and I mean actual surrender, where their planets become yours, NOT just a "they stop fighting back as hard" cutoff), probably based on culture. I want a better pirate system, not this once-per-15-minutes thing, and using pirate capital ships. I want one-note vessels (the minelayers, and siege frigates) to have more abilities so that you have reason to bring them along with a fleet, in the same way that scouts gained their minespotting ability in Entrenchment. And I want a pony.