This might just be me being me, but please bear with me.
In GalCiv2, when you use a Spy you place them on a planet on to a particular building. When she/he/it is placed, they begin to siphon or reduce the efficiency of said structure each turn until the other faction performs counter espionage to remove them. While they do this, they also increase your intelligence level allowing you to see more info over time.
So here is my suggestion, if I may make one: Instead of having multiple abilities you pick to use, have toggled abilities that perform a variety of things depending on which abilities are researched for the Envoy ships.
Some Examples:
- The Envoy ships siphon/reduce planetary credit/resource income.
- The Envoy ships slow research time based on the number of labs at that planet.
- The Envoy ships slow the spread of culture from a planet.
This is far from a perfect system, but it's just a concept. Have at it, I just had to put this idea out there.