I've been doing some thinking about the current DA spy system, and this is what I think.

First:
I don't like being required to disable tiles to place my agents. Having a spy in your empire provides enough insentive to have them removed, let alone what disabling tiles does inaddition to that. This also prevents you from spying on, and stealing techs from one of your "allies" without disabling some of their tiles in the process. What I'm suggesting is allowing you to have the "option" to place spies in other empires instead of on tiles.

Second:
Shouldn't you be able to do more with your spies than merely gathering intel, stealing techs, and disabling tiles? For example:
-Sow discontent, reduces the morale on the given planet.
-Cultural warfare, increases your cultural influence on the given planet, possibly to the point that they begin to flip.
-Insurrection Tactics, reduces loyalty on the planet by encouraging the locals to actively oppose their government.
-etc.

Third:
Secret police. You heard me. Use your agents to support your empire. Examples include:
-Improve Loyalty, silence those annoying opposition leaders by making "disappear". I'm thinking free cable. They'll be too busy watching TV to cause me any trouble. If they turn into some sort of freakish Zombies because of it, even better.
-Cultural Growth, make the planet the site of many rock concerts, or movie filmings.
-Boost morale, free icecream!
-etc.