@AntiBody, awesome ideas. I would like to add to that, the ability to plant spies on specific alien planets, on starbases, and even on enemy ships that pass through your space or near your ships/starbases, maybe via trade routes with them. (These would of course requir ea resource expendature and appropriate tech.) Then you could select those enemy "objects" (planet, ship, starbase) and deliver orders to your spies accordingly. Maybe basic spying (info-gathering) would be automatic on the object you've planted a spy in, while more advanced actions (sabotage, tech stealing) require more spies and more research down the Espionage tree. Of course, if you destroy the ship or starbase, you lose those spies -- themselves being a valuable resource -- but such action could turn the tide of war when executed at the proper time.
Maybe for ships and starbases where you've planted a spy, you see what they see, as well as know the details of the object. For planets, you can't (logically anyway) see all the space around the planet in great detail, but you can see details of the planet's surface; view it as you'd view your own.
And of course you'd need counter-intelligence to defend against these actions, essentially planting spies in your own planet populations, starbases, and ships to try and catch enemy spies. Maybe counter-intel could be automatic; if you try to plant a spy in a starbase that has a native spy already there, for ex., your spy is caught, interrogated, and executed (oh crap, you just gave the enemy crucial intel!). Of course, this may depend on reletive espionage/counter-espionage tech levels, and perhaps starbase/ship modules, and planetary improvements, much like weapons-vs-defenses arms races.
The possibilities are hurting my brain. Hopefully someone at Stardock is reading this thread.