Alright, there have been many, many threads/posts about improving the Espionage system in DA. Well... I figured I might as well go ahead and post my own:

In my system, you assign espionage spending as you normally do. However, you can also make a lump sum payment to immediately finish an Agent's training (like you can do with building ships/improvements), but it would be very expensive.

Agents have three, distinct roles they can preform:

1. Internal Security
All currently Inactive Agents act as a Internal Security score, of sorts. Each inactive agent a Civ has gives them a 5% chance to detect a Spy or nullify a random detected spy/saboteur. However, the maximum number of agents you can detect/nullify per turn is limited by the number of inactive agents you have. Of course, you can also expend an
agent to automatically nullify a specific agent.

Thus, a Civ with 5 inactive agents has 5 tries at 25% chance each to detect a Spy OR nullify a detected spy/saboteur. Note, the Civ has no control over whether agents will detect agents or nullify agents, nor do they have any control over what agents will be automatically nullified (to encourage Civs to expend agents to nullify agents disrupting key planets/improvements)

There is also a small chance (2% per inactive agent?) That you will lose an Agent whenever you successfully detect/nullify a foreign agent. Thus, even if you don't send an agent to nullify a foreign agent, you might lose one anyway when it is automatically nullified.

The increasing chance to lose an agent with large numbers of inactive agents is to force a Civ to have to keep spending money on Espionage to replace lost agents to maintain his high Internal Security.

Obviously, this idea is an extension of other's ideas for Internal Security spending/sliders and Defense Agents worked in to fit better with the Espionage system as it currently is.

2. Spy

A Spy is sent to a foreign Civ to try to establish Espionage contacts and gather information. Essentially, this would work as the espionage slider for each Race did in Dread Lords, except with assigning/removing agents instead of adjusting a slider.

You could assign up to three 3 agents to Spy on a Civilization. The speed and the maximum espionage level you could obtain depends on how many agents you place:

No agents would be necessary to maintain a Low Espionage level, but you also can't gain any espionage level without placing more agents.

1 Agent would slowly work his way up to giving you a Low Espionage level and could maintain a Medium Espionage Level by himself. A single agent can't give you a Medium or High espionage level by himself.

2 Agents would quickly work their way up to a Low Espionage level then slowly up to a Medium level and could maintain a High Espionage level by their selves. Two agents can't work their way up to a High espionage level by themselves.

3 Agents would quickly work their through Low Espionage level to Medium, then slowly work up to a High Espionage level. Once a High level is obtained, one agent could be reassigned, since only 2 are necessary to maintain the High Espionage level. Maybe having 3 Agents maintaing a High Espionage level could give you a chance to gain research data (as the Advanced Espionage level did in DL, or see my other idea below).

Agents sent to Spy on a Civ aren't immediately visible to that Civ. Instead, there is a small chance (depending on their Internal Security) they will be detected. Once they are detected, they can be nullified as normal.

If a Civ has one of his Spies nullified to the point that he can no longer maintain a certain Espionage level, he immediately loses the level and will have to rework back up to the level. However, if he chooses to remove agents, the espionage level will slowly degrade instead of immediately dropping, but once a espionage level drops, he will have to place agents again to work back up to the desired espionage level.

I basically got this idea from one of the old preview screen shots of the espionage screen in the Domestic Stats window. In fact, this is basically how I thought/was expecting the information gathering would work with the new Espionage system based off that screen shot.

3. Sabotage
This works as it currently does. Agents sent to sabotage can't establish or maintain Espionage Levels by themselves, although they help Spies attain one faster.

Saboteurs are immediately visible to the defending Civ (as they currently are) and have a chance to be automatically nullified depending on that Civ's Internal Security and the Spying civ's espionage score.

Notes:

1. Civs with a Very Low or a Low Espionage level with you would have a rough idea of how secure you are from their agents (IE: They would see something like... HIGH internal security or VERY LOW internal security). Medium would give a number estimate, that could be off up to 3 agents (thus, if a Civ has 7? listed for its internal secuity, it might actually have 4-10 agents.) High would give an exact number of inactive Agents.

2. Because you have no control over what your Internal Security does, not to mention the fact that you might lost an agent anyway, expending agents to nullify an agent still has a purpose. The Counterespionage Center that's planned also still has a purpose, since it not only makes a planet immune to sabotage, but it also lets you save agents for other purposes.

3. Personally, I have no problem with letting some agents sit on my planets for the most part. As long as its not a key building or crippling the planet's usefulness, I can leave it be. After all, if a factory isn't working, I'm only losing the production, but I'm also saving the money they would have otherwise been spent towards it. I think
that just like the Yor Super Ability problem (ie: the stupidly high speed ships being reduced to 3 movement "problem"), truly new players will be able to deal with Agents much better (and with less complaining, no doubt) than players who are used to getting the full benefit of ALL their improvements, ALL the time.

4. Being the top Civ shouldn't make you THE biggest target for Spying/Sabotage. A bigger target, yes, but the AI should also use its spies to disable foes they are in direct competition with first before trying to bring down the big dog from within. I think this alone will greatly reduce the negative comments about the Espionage System as is since many players remain the top Civ for a good length of time.

5. It would be neat if there was an Invasion Tactic that tied in somehow to your Espionage/Agents (or just see my other idea below ).

6. Agents that you remove shouldn't be immediately placed back in your Inactive Agents. Instead, you would get them back at the beginning of your next turn (grey them out on both their current location as well as added a greyed out agent to the Inactive Agents list to represent this).

That's it. I think it fits in well with how the current Espionage system is set up and is simple enough to fit in without adding needless complexity.

Well... that's not really it. I do have one last idea that's a bit more complex:

Missions
If you remember Probe Agents in Alpha Centauri (which I imagine you probably do), you should have a basic idea of what I want from Missions.

Basically, Missions would be unique, very specific goals for your Agents to try to accomplish. They would range from... instigating a revolt on a planet via Mind Control probes, stealing technology files, stealing money/ships sabotaging a Civ's Research, sabotage a Civ's relations with another Civ, destroying/taking over a starbase, to assassinating key government officials, disrupting their government and forcing a Civ to have to operate in a Imperial goverment for X number of turns. Essentially everything else players may want to do with their Espionage spending. Missions, like Invasion Tactics, might have Tech Requirements before they can be performed.

Each mission would have a set percent chance to succeed, modified by the defending Civ's Internal Security and the Spying Civ's Espionage. Each mission would also have a required number of Agents needed to perform it, but you can assign any number of agents to a mission, and each extra Agent increases the Mission's chance to succeed (although, each Agent assigned gives diminishing returns in this matter).

If the Mission is successful, the effects are applied. Missions could potentially be a very powerful tool. However, its not without its drawbacks. First and foremost, all Agents sent on a mission are automatically lost, whether or not the Mission is successful. Secondly, unlike Spies or Saboteurs (as above), sending agents on a Mission carries the risk that the defending Civ may find out who sent the agents. The more agents sent on a mission, the larger the chance the Civ will figure out it was you. Naturally, the Civ is not going to be happy if they find out you sent agents on a mission against them. Of course, you can always try to have your agents blame the incident on another Civ... *grins*.

Overall, the biggest, baddest Mission available would be the Espionage Victory. Yep, a big, huge Espionage project that the ultimate goal of is Intergalactic Domination. It would be a combination of assassinations, mind control probes, and general mayhem... think Evil Geniuses from Bond and the like. The project would have very little chance to succeed without a huge expense of agents and other resources, but obviously, if successful, it would win the game. If its not... well... everyone is going to HATE you.

Well, now that's truely everything I have to say about the espionage system.

Comments and other ideas (especially ideas for missions!) are welcome and greatly appreciated.

Edit: Cursed formatting tags!