I'm hoping htese are kind of a cross between Capital ships and lesser ships, with perhaps several skills that can be increased.
For example, a Vasari Envoy cruiser might have "Privateer" "Assasin" "Spy" and "Steal" skills that it gives a bonus to using against the planet it's orbiting. Steal would allow you to take resources from the faction you're using it against, Assasin would allow you to kill the governor of a planet your'e orbiting, resulting political chaos and confusion would reduce that planets loyalty and efficiency. Spy allows you to steal technology, giving you a jump in your research, and Privateer, a higher end skill, would allow you to make a limited size fleet the Envoy Cruiser is part of look like pirates for the duration it's in an enemy gravity well...allowing you to attack friends without starting a war...Vasari aren't nice 
I think in combat Envoys should be powerful ships in their own right, not up to Capital firepower standards, but very durable and something that's worth micromanaging individually. They have to protect the Envoy, Ambassador, etc after all! They should be more limited than even capital ships in terms of numbers you can build however.
Naturally missions to bring an Envoy cruiser to specific meetings with a limited amount of escorts to protect both sides forces should be available, and there should be the option to hire Pirates or third parties to ambush such fleets.
Planetary Economies would be more interesting if they have more variety, so some planets would be extremely important to capture, having each planet being generic and the same can reduce the fun of exploring the system. At least have this as an option for universe creation.