The basic concept is to combine the spy systems from DL and DA, but with some enhancements. I know it's a bit complicated for GC 2, but it's an interesting thing to consider for future iterations of the series.
Basically, it goes like this:
1. Total Espionage budget is increased from 25% to about 30% for the reasons that will be extrapolated below.
2. The single Espionage slider is replaced by two sliders. The first sets the percentage of the budget spent on intelligence activities. The second determines what percent of that Espionage spending is devoted to Intelligence gathering, and what percentage is devoted to Agent Recruitment
Example:
Espionage
<-----------> 500bc
? <-----*-----> ! 250 bc Intelligence, 250 bc Recruitment
3. The single Espionage tab under Domestic controls is replaced by two tabs: Intelligence and Recruitment. Both tabs include "telemetry" of the Espionage sliders, so that the budget spending can also be changed on that screen.
4. Intelligence, or passive spying, works like the DL system. Money is spent on raising your Intelligence level on a certain civilization: at a certain amount of spending, your intelligence level goes up. You can also reduce the intelligence that foreign powers have on you by devoting part of your budget to Counterintelligence. Foreign powers can do the same to you as well.
5. Recruitment, or active spying, works like the DA system. Money is spent on recruiting agents who can then carry out several different missions. These missions can be chosen from the Domestic menu, or (for certain missions) from the screens indicated below.
-a. Defense: Agents not currently assigned to a mission are placed on defense. Defending agents provide a bonus to the civilization's Counterintelligence score and are required to neutralize or convert foreign agents.
-b. Sabotage: the current DA spy mission. Can only be chosen by clicking the "spy" tab on the galaxy map. Shuts down a building's production. When the mission begins, the target nation immediately knows what has happened and must "spend" a Defensive Agent to neutralize the saboteur. Requires at least Low level intel on the target nation.
-b. Steal Technology: Can be chosen from either the Recruitment screen or the Foreign Affairs screens. An agent is dispatched to steal a random technology from the target nation. When first assigned, the foreign power is not aware of the spy: the spy must first be identified before it can be neutralized. First, the civilization's Counterintelligence score gives it a chance every week to identify an agent trying to steal technology. Second, if the agent successfully steals a technology, it immediately becomes identified and can be neutralized.
(This system basically would tend towards a strategy of: place agent, wait until an agent steals a tech, recall them, then immediately reassign them, thus setting the counter back to zero. My suggestion is that an agent used to steal technology can't be recalled: imagine an American weapon's scientist being courted by the KGB. The moment he was identified, he became useless as an intelligence asset. Even if he had been rescued by Soviet agents and given a nice dacha near Moscow, he would have been useless for the purposes of stealing more technology from America.)
-c. Degrade Relations: Can be chosen from the Treaty screen, where it shows relations between the target nation and another one. Basically works by spreading disinformation and propaganda to cause relations between two nations to falter. Agents are identified using the average Counterintelligence score of both nations. The higher the relations between the two countries, the harder it is to degrade.
In addition, neutralizing an agent once Identified has more options than the standard DA system.
1. Wetwork: Calls up an "Engineer" to "Troubleshoot" the situation. Spend one agent, and the enemy agent disappears. Where did he go? Better you don't worry about that, sir, we'll take care of the dirty work.
2. Double Agent: Costs some money based on the spy nation's base Loyalty scorevs. your Influence. Through bribery and persuasion, you convince the agent that it can be more profitable to work with you instead. Provides a bonus to your espionage level on the target civilization. However, the downside is that the foreign agent must remain in place to keep his superiors from getting suspicious.
3. Defect: Costs even more money, also based on the spy nation's Loyalty vs your Influence. You buy off the enemy agent and convince them to work for you instead.
4. Diplomacy: Not exactly an Espionage option, but one you can use from the Diplomacy screen. You talk to the foreign leader and you ask them to remove their agents. Depending on how interested they are in keeping you happy, they'll do so or refuse. Some persuasion may be necessary.
. . . now that I think about it, this may be way too complicated. This is GalCiv, after all, not Spycraft. . .