AdmiralWillyWillber, we appreciate suggestions, but have you actually played the CU mod? 
I don't think replacing whole diplomacy tree for Korath/Drengin/Yor is a good idea, as this would require all diplomacy techs to be made untradeable, and I think most of us would not want to reduce tech trading anymore. Only thing that could be changed is the name and descriptions for them (Basic Diplomacy and Alliances could be redone, I think rest of the techs should stay as they are), so feel free to write up some replacements, and if rest of the crew working on CU likes them I'm sure they will be implemented.
how about giving the yor a few more economic buildings, or making the efficiency center a building instead of one per planet, and making them upgradeable
That would make them behave just like any other race, which I don't think is a good choice. Yor economy is unique to them, and it should stay unique. To help with their economy they now have access to government techs, also bonuses from Efficiency Studies has been almost doubled. They also get morale bonus from Charging Stalks techs. They lost Efficiency Center, but overall their economy is better then what they had in vanilla.
Yor and Korx mostly got buffed in CU, they are in good position and I do not think they need any additional techs or bonuses. We do not hate Yor, on the contrary, at least me and Maiden like Yor more then other races 
Not sure about Drath, as I don't play them, but they have been tested thoroughly when they had big changes in one of the earlier versions and no one noticed them being weaker compared to other races. They just rely on their Super Ability a bit more.
While there are still some civs that are stronger then others (Thalan for sure, probably Iconian and Torian), any nerfs to them could easily make them "coinflippy", playing very good in one and totally bad in another game. From my experience, Thalan are really hard to play early as they are, especially on galaxies with fewer worlds and slower research speed. Their economy is hard to handle initially, but they shine on larger galaxies with higher number of planets. Iconians are more or less the same. That's why I don't think anyone want to go down this road and fiddle with balance again
I guess if you remove espionage from krynn's spy training center's then you should rename them, and move them to the research tree, or give them some other spy bonus.
Those techs only provide really small bonuses to research. Espionage bonus was removed because it has negative impact on AI economy management. Maybe it should be brought back in some way. Krynn's racial Espionage bonus can go down from 50 to 25, and the remaining 25 Espionage could be distributed between Superior Espionage and Master Spies (or the SPs/GAs provided by these techs). It will help AI with economy management, while at the same time make those techs do what description suggests.
Hmm. Perhaps a compromise is in order. It is true that the beginning CU/Weapon Cycle player is no worse off than the AI, which does not pick a specific weapon line based on an overall weapons analysis as far as we can tell. But if we give them hints that not all weapons nor tiers are equal, they may take it upon themselves to do a straight-up comparison and discover each tier and weapon line's strengths and weaknesses for themselves. If we don't give them hints, we are going to end up with a lot of hate and confusion over "unbalanced" weaponry. I'd prefer to nip that in the bud.
Mabus mentioned he is working on a new manual, so you can safely mention new weapon system there :>
