New uses of Agents:
In the current system, agents are either placed on specific buildings on planets to shut them down, or placed within empires in general to gather overall information. In addition to these locations, here are a few other ideas for places to send spies in enemy empires:
Research: Spies in enemy empires could either give their source empire a percentage of the enemy empire's research (sort of like a research treaty), or attempt to slow down enemy research. To me, the first is preferable, since the enemy empire's research would not be reduced, and thus spies would be more difficult to detect, but both methods seem like potential uses of spies. they could also both be offered when a spy was placed in an empire.
Military: Spies within an empire's military could either give combat bonuses when fighting that empire (the idea being that spies have discovered the empire's typical strategies and fighting methods, so they can be countered), or simply reduce overall military strength. As with research, I prefer the first option, but both seem potentially plausible.
Economy: As with research, spies could either siphon income, or reduce the enemy empire's income. My opinions are the same as with research.
Morale/Loyalty/Influence/Production: In these cases, it's hard to think of a plausible backstory reason that spies could "siphon" these from enemy empires, so the values would probably just be reduced throughout the empire.
Spies could also be assigned to counterespionage, where they would reduce the effects of enemy spies within your own empire. The effectiveness of your own spies at negating enemy spies would be based on a separate counter-espionage rating (for example, if one empire has twice the counterespionage rating of another, the first empire's spies would be twice as effective at neutralizing enemy effects as the first empire.) Spies might either be sent to negate (or attempt to negate), the effects in a particular area, or into counterespionage in general, where their neutralizing abilities would be spread throughout all categories.
Counterespionage center type buildings on planets would help reduce the effects of enemy spies for that particular planet, either by counting as a particular number of spies, enhancing the effects of spies already in counterespionage, or by a simple percentage. Spies could also be placed on particular planets to provide counterespionage for that particular planet.
When used to eliminate enemy spies, each friendly spy could eliminate one enemy spy. The friendly spy would have a chance to survive based on the friendly counterespionage rating. the chance would likely be adjusted so that killing enemy spies would have the same overall effect as passive neutralization with counterespionage.
Spies on specific planets could have a similar effect as spies in the entire empire, though would siphon/reduce production by a higher percentage (Probably based on map size) than spies in the entire empire.
In addition, spies could be used to attempt to sabotage production efforts for a turn. The chance to successfully stop production for the turn would be based on the planet's spy defenses, both from empire wide counterespionage, and counterespionage on that particular planet, and the amount of spies attempting to sabotage. The actual chance for sabotages per spy would depend on balance.
In the current game, espionage rating makes espionage spending more effective at producing spies (I think). I could see either keeping this system, or having espionage rating change the effectiveness of offensive spies.
(The link is to the original place where i wrote this idea out.)