I love having tech brokering off - it makes it fundamentally easier to work techs tactically if they don't go any further.
Spies definitely need to be removable - on one hand, it makes more sense to me that to have up to date data you have to have people working all the time, on the other hand, I got four analysts on a civ and lost them all when the civ surrendered to the Krynn. But other than that, I'm fundamentally happy with the spy system.
Planetary Governors definitely need a little more work, because as it stands, planets are so varied that the "wish list" just barely cuts it.
A. You should be able to save lists between games, associated with the tech tree it uses.
B. Ordering needs to be more intuitive;
C. You should have a 'default' initial governor based on planet size; set by the user - I may want a specific governor for planets below <=6 from 7-11, then from 12 to 17, 18 to 24, and above 24, or someone else might want something different,
D. it needs some very minor scripting functionality. I understand you don't want to do this, but I REALLY REALLY want it, because it needs to be able to do so things like "if planet has a +400% tile, go ahead and build a research center" and "First build four factories. Then upgrade them one by one until we have four industrial sectors. THEN build a starport, then spam the econ buildings, and don't build the xenofarm till last".
A-C shouldn't be hard I should think, and would make it more useful. D may be more than you want to do, but would make it incredibly useful.