First, I'd like to say that there are several other threads with a similar topic. And that it would be nice if we could consolidate them into one big sticked "Espionage Ideas" thread.

So now onto my own thoughts. Also, some of these ideas based off ideas from others who made posts in other threads.

The current system is simple and works well, or it will once its tweaked and balanced properly I suspect at least. But (yes there it is, but, what an ass of a word) I want some more meat on my bones, and I think more depth could add alot to the game.

Basics
There should be two sliders, one Espionage, which is the amount of money being pooled into training and recruiting new spies, as well as their funding for missions. Secondly, one for Internal Security, which determines the level at which you control you're empires inner workings. In essence, Espionage is your offense, and Internal Security is your defense, the biggest difference however is that while espionage only takes away from your income, internal security damages many aspects, your morale, trade, population growth, and anything else that would stem from a highly controlled and freedomless society.

Espionage
Once you have money funneling into your espionage program, you can recruit agents, these are 007 type agents, deadly, capable, and professional. Agents take several turns to recruit, and get progressively more expensive, and take longer to acquire with each additional spy. In the beginning, they are medicore but can gain experience and become stronger. There are two ways this occurs, either by having agents completeing missions or having them train in the safety of your Intelligence HQ. The tradeoff being that you cannot recruit other agents while this is occuring, only one can train at a time, and it takes awhile to do.

So what can these agents do you ask? They have four possible objectives:
Sabotage - You destroy a facility, ship or starbase.
Infiltrate - You can enter a facility to divert some of its production to you, a ship causing it to be less capable in all aspects (speed, range, weapons etc.), or a starbase where its effect decreases in potency and can even become a hindrance. In the case of resources, part of its bonus is diverted to you. Unless the player notices, or his internal security detects it, this is completely transparent and invisible to the target.
Steal - Allows you to steal ships, resources, and techs.
Corrupt - You enter a planet and attempt to bring its government under your control subvertly, slowly lowering its morale and influence and potentially causing it to revolt to your side. You can also use this ability to sour relations between the target, and any race he has come into contact with. This starts slowly and builds, like infiltration it is completely invisible aside from its effects.

Each agent, specializes in one, or is a jack of all trades. There is a percent chance of success for each one based off the agents level of experience, your espionage funding, the targets internal security rating, and your espionage tech level.

Sabotage is the quickest to accomplish, and generally has the highest success rate. Infiltration lasts as long as you assign the agent to that task, if he is on a ship/starbase that is destroyed, he usually "escapes" before hand, it has a moderate success rate. Stealing is quick like sabetage, but has a low rate of success due to its overall difficulty. Corruption is the most difficult task, due to all the factors that can go wrong, it has a very low success rate and lasts as long as the agent is assigned to it, once the agent stops or is caught, the planet returns to normal over several weeks.

Internal Security
The higher this goes, the better chance you have of catching spy acting against you, or even before he can begin his task. By controlling the populations lives you can more easily discover those attempting to subvertly damage you. At the highest levels, only sabotage has any chance of success due to its quick and somewhat simple nature, but even then the chances are slim. With no Internal Security other races and do as they like with you, unless you get lucky, chances are more devious races will blow up your stuff, steal your techs, and turn your own planets against you on a regular basis.

The levels of security are as follows:
None - Completely open, no security in place. You get a morale bonus, trade, and a population growth bonus.
Low - The default setting, your society is open, but you do have measures attempting to catch spies. No penalties applied.
Moderate - You exert control over trade and the media more tightly, and you seem to have a mild obsession with security check points. Morale and trade penalties.
High - You further demand your peoples obedience, and reports seem to show that you like cavity searchs a bit too much. Morale, population growth, trade, and production penalties.
Extreme - Barcodes for everyone and random raid tuesdays! Population growth, production, research, and trade penalties, with a major morale penalty.

When you catch a spy, there are a couple of possible outcomes, the most likely being that he escapes or is killed. He can also be captured and interogated, revealing who he works for. The least likely, however, is that he'll "turn" and become your agent.

Other effects could be played out, such as alignment, and diplomatic relations. But I'll leave those be for now.

Additional Thoughts
A variety of other factors could determine how successful a race could be, such as level of diplomatic relations, trade levels, and influence. All of which would logically make landing spies easier, or harder depending on how strong or weak your level of interaction is with the target.

The Super Spy ability would allow a player to set higher levels of internal security without penalty, or with severely lessened penalties. Espionage ingeneral also would cost less.

Techs would exist to give bonuses to certain objective types, as well as helping defend against potential threats.

Maybe you could make espionage pacts, allowing you and an ally to team up for espionage and counter-espionage.

If heroes were ever introduced, spies could assassinate them.

Espionage should generally be less about micromanagement, and more about assigning spies to do a task. Basiclly, I want internal security do most of the work without my hand in defending against spies. Sure I can opt to send a spy to try and defend something from other agents on occasion, rather then have to play "Whack-a-Mole" but with spies rather then moles and a hammer.

Because of spies more grand role and greater potential, the number you have is very limited. Most likely by techs, spending and maybe a super project. I foresee 5 or so being a lot of agents.

Every mission or task assigned to an agent takes a certain number of turns, which can vary dependent on spy level, tech and so forth. Spies could also cooperate on an assignment lowering the time it takes, while also raising the chance of being caught.

I considered for a moment sabotage, and the fact that an enemy could simply replace a building, with generally lil cost or worry beyond its basic destruction. But consider the fact that if you had several spies, they could all hit say the factories of a planet simultaneously. Effectively you could shut down a planets production capabilites, and force your opponent to up his internal security and/or place his spies on defense. Thats a powerful effect.

In closing...
Yes I know this is fairly complicated, and would be a nightmare to code for the AI to use effectively. And the current system is sufficient, but it would be fun however to see it evolve over patchs to something like, or at least as deep or deeper then what I've concocted in my head. With a strong espionage backbone, you should be able to do impressive things, but always at great risk and cost. Anywho, those or my two lonesome pennies worth of thought.

Thanks for reading, cause dang, this thing got long! >.<

EDIT: Added more to additional thoughts.