So I have a few ideas about how espionage should work instead:
Finance
From whatever primary financial control is offered, espionage should have its own slider for the percentage of income you want to throw into it. This would probably be a fairly low percentage unless spying is a huge source of power for you.
Recruiting spies
The recruitment and training of spies would be done automatically by your intelligence leaders. Instead of having lots of individual spies with their own stats you would simply get a number indicating how many spies you have, and the average stats of them all (as spies really would be trained to a consistent standard).
Counter-espionage
This would be done simply by doing nothing, by default all spies not on a mission look for signs of enemy spy activity and generally help co-ordinate police forces, security teams and ship-board security efforts in keeping spies out.
Sending a mission
Idle spies can be sent on missions against enemy (or friendly) races by changing your spying options for that race. When you choose to alter these settings you would get a number of options, first and foremost is a slider bar indicating what percentage of your idle spies you want to send against this empire.
Secondly you choose what mission types your spies are to attempt, a few ideas are as follows:
Science - concentrate on damaging enemy research, stealing research items, destroying labs, killing scientists etc
Military - damage production of military ships, attempt to sabatoge defensive fleets, scramble enemy communcations (so they don't detect enemy fleets as early as normal).
Political - damage relations between the target empire and other empires, frame them for supicious acts (e.g link them to terrorist attacks), assasinate enemy leaders
Social - attempt to cause unrest or revolt by destroying entertainment facilities, setting explosives in public places or causing bomb scares. Could go as simple as putting rude grafitti everywhere
Economic - damage trade relations, space ports, alter ledgers, divert cash flows or just set fire to people's wallets. Cause monetary woes to the enemy.
Intelligence - by getting involved with the scum and villiany of an empire you can get a good idea of what that empire is doing, this information can allow you to detect enemy fleets earlier, stop enemy spies more easily or discover certain interesting projects or deals being developed.
Havoc - everything is a target, and you've got the trigger. Just blow up anything and everything and see what happens
These options are important and multiple choice would be allowed. Obviously choosing only a few areas of attack would allow you to do better at those tasks. The exception is havoc which is an option that allows no other choices to be made as it covers them all but in a more destructive way than selecting them all minus Havoc.
A further few options could be available too:
Risk - how far your spies should try and go. The higher the risk is, the more chance there is of your spies getting caught, but also the greater the possible reward. A high risk could allow you to do a much larger number of nasty little things in a single turn.
Damage - this would probably come in specific levels. The damage value determines how many civillian casualties and overall devastation your spies cause. Setting a low damage level will tend to have your spies concentrate on targets within a building rather than the building itself (e.g killing or capturing scientists instead of blowing up the lab they are in).
Generally the lower the damage is set to, the higher the theft becomes as your spies attempt to covertly steal things as an alternative to having a bit of fun...er...I mean damaging things.
Interrogation
When enemy spies are caught then some of them may be captured alive for interrogation. The more enemy spies you manage the interrogate, the stronger you become against further enemy spy attempts (e.g forcing information about planned attacks out of a spy). The only way to get around interrogation and the negative affect it can have on your spying attempts you have to set a lower risk level for spies in that empire.
Conclusion
To me this method of controlling spying seems much more fluid and simple while still being fun and retaining a nice degree of control. In MOO2 and MOO3 I hated having to build/train spies and send them out individually.
