| it might be worth considering an espionage module for ships |
This is exactly how to handle it.
Attach spies to freighters. With miniaturization, you might be able to add another spy module. The key with the module, as with troops, is that you need an available spy to put in the module.
Between the cap of 12 trade routes and miniaturization, no civilization will be able to have more than 24-30 spies.
This controls how fast spies infiltrate a given planet and prevents spies from over-taking the flow of the game. As more spies arrive, a given civilization should be stronger.
With a limit, we enter the realm of strategy.
I would have no problem with spies under this kind of setup. It needs refinement, of course. However, I believe that GW has given this game an opportunity to break the impasse between developers and discontented players.
One thing I see with the spy module: players need the option to redirect freighters if the spy situation calls for it.