From what I read here, you might would like my following idea of a more event driven system for the spies. Has somebody played the game Hearts of Iron III? Especially the Mod Black ICE. The game is full of events in which you can choose to apply different decisions which grant bonuses for units or policies. It is something like the Events & Decisions Mod on steroids.
The Spy Menu:
Leave it unchanged like it is at the moment..
Events & Decisions:
Gazebo implemented some events in which your spy was able to delay the production of a city or he was able to steal some gold. Why won't we take the random events and put them into a window where you can decide what he should do:
On the screeshot above, you can see a typical window which sometimes appear and where you have to make a decision. So there for example, you could get a message, that your spy made some investigations and some preparations in order to steal a technology. He says that he would need 40 production of one of your cities, or 100 Gold, or 20 science, or whatever in order to conduct the coup. So the system could be based on paying something in order to conduct the event. It would then happen or not. The possibilities for those events could be taken from what Gazebo calculated or by new considerations. Because the system is about taking decisions you will also have a second option like refusing the coup, or a third option in which you say "Ok, I pay x amount of x in order to make a more successful coup. This could be like a Tier system.
The Tier-System:
The events come from a event pool, so once the general system is inbound it would be easy to introduce new events like it is actually in the Event & Decision Mod.
There could be, for example three Tiers of decisions. They are sorted by a theme, for example the Tech theme. The next tier will be unlocked by investing a specific effort into the decision, so the next tier will be more powerful and maybe more successful that the tier before.
Example (Tech Theme), your spy reports his status:
- Tier 1: "I found a way to enter their research lab, I am now employed as a scientist. Maybe I could make some trouble by being awkward, or if you would give me some
Gold I could try to get an employment in their research department. Then I could have access to their latest research project and I could boost our research with their insights."
Possible answer:
- Ok this is enough for the moment, let some bottles fall or let their lab go up in flames. Science is a dangerous activity. [The nation of this City will loose a specific amount of
science]
- Take that Gold for your further education and try to enter their research department. [Pay 100
Gold for this spy]
- Don't do anything dangerous, we have to wait for an opportune moment. [Your spy will do nothing]
- Tier 2: "I made this course for advanced employees in science with the
Gold you gave me. I got the promotion for being able to work in their heart of the research department. They are developing really crazy stuff, I could try my best to steal some parts of their research. It is still too dangerous for stealing their whole technology, I would need some further aids."
Possible answer:
- Try to make some notes. Maybe they will help us at our research. [You will get 100
Science which will boost your current research project.]
- Here are some tools of our latest research. They will make your plans easier for sure. [Pay 200
Production of your capital for this spy]
- Don't do anything dangerous, we have to wait for an opportune moment. [Your spy will do nothing]
- Tier 3: "With the tools you gave me recently, I am now able to unlock their safe where they store their latest technologies. With some
Gold I could bribe the local guards and then I could enter the safe."
Possible answer:
- Steal their technology and do anything necessary [Pay 300
Gold, you could be able to choose one of their technologies]
- Don't do anything dangerous, we have to wait for an opportune moment. [Your spy will do nothing]
Summary
I hope you got an idea of the tear system. For each decision there could be more or fewer possible answers. You could make different themes like the population theme: So tier one could be that you have to pay one

population of your city to send some rebels in order to raise their

unhappiness up to tier three where you could poison their water to kill one

population of this city. There could be a

Gold theme, where you could steal some

Gold at tier on, up to tier three where you could channel off some

Gold each round as long as the spy is in this city.
It is not necessary to have always three tiers, but this is only an example how it could work. With such system you would be more connected to what your spy is doing and you can influence him and his result. By unlocking the next tier you could get a higher reward by paying different things. There are so many possibilities like

Gold,

Production,

Science,

Population,

Happiness,

Food etc.. By refusing a decision their could occur a different theme. So by refusing the

tech theme, you could get a

population theme next..
Every decision and all themes will rest upon the permanent danger of getting caught and maybe getting killed. By taking a decision it will not mean that this event or the next event will be successful. By paying for your decision or for the next tier, you have to do something in order to profit from your spy and his result. The written prices are only an example how it could work.
What do you think? Maybe it could be easily implemented by using the already existing system of the Events & Decision Mod.