Here are my thoughts on the Espionage System so far.
The Espionage System is okay (The little spy icon though with the fedora is VERY cool. Kudos to whoever designed it), but its nothing really revolutionary. I know this is just a beta, and this is why I am posting my thoughts here. These are suggestions, not complaints.
Of course - in all fairness, when was the last time that you played a game with a REVOLUTIONARY espionage system? They all boil down to the same thing. I get a number of spies and either put them on attack or defense. When on the attack, they do bad things to the enemy. The enemy tries to do the same to me. That's it. Spies either work too little mischief (when viewed from the empire perspective) in which case they are useless, or too much in which case they are overpowered.
Sure I would love a James Bond flavour to my ideal spy system. In my fantasies spies would come with their own strengths and weaknesses (kind of like the generals in Rome Total War). I would outfit them with slick gadgets and send them on their missions. Then I would read field reports of their brave exploits, narrow escapes or ... alas - their capture and or death.

When I capture spies I can Interrogate them, Execute them or do a Spy Exchange. There would be a myriad of missions that my spies could go on ranging from assassination, to destroying facilites, terrorism, capturing research, destroying star bases or grabbing ships. But honestly, this is only my ideal system and it would be damned hard to program this.
More realistically, I think the key to making espionage interesting is that it needs to touch another level of the game, and lets face it - when it comes to ultimate levels of the game the political battlefield is god.
So here is what I propose:
1) Spies can either be Active or "Laying Low". They only work their mischief when they are active, but are easier to catch. But catching a spy is not just a factor of how many opponent spies are working security. Its also a matter of the opponents internal security. Internal Security is a slider that can be set on the Domestic Tab. At high levels its nearly impossible for spies to work their mischief, but at the cost of lowered approval, trade income, economic modifiers and most importantly on the IMPROVING of diplomatic relations on other races. So ... If I am the evil JiggyBobs, and am concerned on the growing closeness between the Altarian and Torian sissies, then I can send in the spies. The actual havoc that they wreck is only a secondary objective. I am trying to force these two to increase their security to at least slow down the hug-athon that is going to happen between these two.
2) I think that counter spying should be inversely proportional to how "Big" your empire is. Not only is this realistic, but it prevents espionage from being just another hammer for powerful races to whack those less powerful.
3) I think that landing spies on planets should be a non trivial matter. The factors working against such infiltration should be a combination of the following: Number of military ships in orbit, Number of facilities on the planet (i.e. the beuracracy), Counter Espionage, Internal Security, and that race's influence in that sector. Factors that make it easier to infiltrate a planet would be a combination of the following: Spy level (I think Spies should gain levels), my relations with the race (the closer we are the easier they are to trick), my influence in the area, and most importantly ... whether I have a trade route to the planet. So if there is a manufacturing capital that I absolutely need to sabotage, but can't infiltrate then I have several options. I could put a trade route to the planet, build an influence starbase, or act really friendly to improve relations. Similarly, if they take a planet that has HUGE bonuses on it, then it will be important to land a spy on it while it is in development, rather than trying to after. If I discover that a certain race is causing a lot of havoc to me with their spies, then I can deliberately poison relations, or declare an embargo making it harder for them to land future spies.
4) Lastly, I think that if spies had the ability to poison relations between races this would definitely make things more fun. Of course this should be fairly difficult to do since its so powerful. Also, perhaps the person would need to spend extra money or influence to initiate such a mission. The spy would finance or start terrorist groups that despise the other race and spread racial hatred propoganda. If someone is doing this to me, then on the relations description it should show "Third Party Poisoning" or perhaps "Radicalism".
5) There should be a chance that when I catch a spy, I can identify who sent them. When someone catches my spies and determines their origin my relations should definitely take a hit, though this should be fairly rare, otherwise espionage will be too risky to use.
Anyway, these are my thoughts - though I imagine getting this whole level of strategy to work with the AI could take way too much time and effort.
Dano