[AgentZero]

I like the agents idea but I'm not sure if Aaron is a big fan. I suggested when SE4 was underway and it didn't make it. I rather liked the way Imperium Galactica II handled the concept. Basically you have to build a spy base before you can have any agents, and each spy base can support X number of agents. Unlike IG2, I'd like to see the ability to recruit agents from a 'pool' instead of them appearing randomly. Each agent would give certain bonuses to the chance of success for a intel op.

Another little idea, if the idea of Captains makes it into SE5, I'd like the ability to assign spies to your own ships. This would work in two ways: 1) If you assign a spy to a ship that already has a captain, then the spy acts to detect and halt intel ops against that ship.
The second way would require a whole new tech area: Spy Tech. Aside from general advances that would increase chances of success/decrease time & cost, (& maybe implants to cybernetically increase an agents abilities) there would also be ship components basic ones would make a ship invisible to the enemy (regardless of sensor tech. Other spy ships would be the only real way of finding other spies). More advanced components would further increase the success rate of intel ops. Of course, the only reason this would make sense is if agents had to actually enter enemy space in order to perform certain ops. Some ops, like those against planets wouldn't require a spy ship to be sent in, since there's other ways for a master of disguise to enter enemy territory.
Speaking of disguise, if we have agents, one would assume they would be from different races. Thus, using an agent against an enemy of the same species would increase chances of success but his loyalty would be suspect.