1.) The problem with spies is that so many improvements have been made spy-proof. It will take serious modding to straighten this out. Were I still running an XP machine, perhaps I could just alter the Improvements file.
2.) This can only be corrected by Stardock.
3.) I really need to explain this:
The earlier versions of ToA differentiated tech development so that the different empires would progress differently at different speeds. Some empire's would have massive advantages early in the game, only to be handicapped later on. Balancing this kind of game is a delicate thing. We all know that some advances in technology come at a price, some are simply better in every way, and still other technologies retain their advantages century after century.
Had 2.20 improved on this idea, the Iconian Empire would have lost the ability to perform research along the lines of other empires. The Precursor Archive may have been improved, while the library transformed into a mundane improvement. Some other type of improvement may be added to supplement research, but they would not be able to research Academies, Invention Cities, and Discovery Spheres. Having access to the knowledge of the ancients is an early advantage, but having one's questions so easily answered comes at the cost of never learning how to answer those question on one's own.
The 2.04 Version of the game allowed for quirks in technology. We saw this in engines, where the Ion Drive was never completely outdated. The five steps in Warp Drive technology provided some interesting quirks. The differences between Disruptors and Phasers could have probably been better balanced, but giving all races the same weapon trees just makes for a dull universe.
btw, What happened to I-Mod's Tech Tree Viewer? Until I can recover my old HD, I can't look at any mod I create. At this point, all I can do is try to demand something better.