Hey there, I noticed that you are a little light on the Trek side of things so I figured that I might as well toss in a couple thoughts.
I saw some very good ideas on trek propulsion a few pages back that seems perfect (posted by SuicideJunkie I think). Only problem was that those designs were based on standard movement (more appropriate for trek I think)not Q-N. Is that a problem? Can you have multiple propulsion types like that in the same mod?
The way you seem to be doing things (with each race having its own tech trees and such) this doesn't seem to be too much of a problem. Then again, what do I know, all I have to play around with is the demo (at least until gold comes out). Though, if you could maintain both types it would go a long way towards giving a unique star trek feel to their races.
I was also wondering if there was a way to have central tech areas where each of the individual races could branch off of instead of having multiple redundant tech areas for each race. For example, instead of having Federation ship construction, Empire ship construction, etc., you could have every race research "ship construction" (modifying the tech area so that it is empty, ie. provides nothing for researching it by itself) and have each ship require the appropriate tech level of ship construction *and* a single level in "Klingon Tech", "Rebel Tech" or whatever.
These race techs could be limited to only one level (or more) that is automatically given to a specific race (starting level 1). This could also be used to tie other techs together, like beam weapons, propulsion, etc.
By now you may be asking yourself "Why in Hell would I want to do that?". Well I'll tell ya. So far as I've seen you've gone to a great deal of effort to balance out the various techs while allowing each race to maintain its own style. This is good and is the entire point of doing a crossover mod. The problem that I see is that with the current setup one of the key aspects of the game has been removed. You can no longer trade/steal/reverse-engineer tech. If all tech areas are racial then they cannot be shared with other races.
I have heard that if you remove the racial number from a racial tech area then it can be learned by anyone who gets their hands on it ( though they can't initially research it). While this option might be a good idea for certain techs I think that it would be a bad idea for the basics. After all, having Ferengi cruising around in star destroyers of their own design is just wrong. Not to mention that you could wind up having ten different ship construction areas in your research areas. That could get annoying.
However, if you have things based off of a single tech tree (as I tried to describe above) you could have the Narn analyze a captured galaxy class ship to give them ideas on how to create bigger ships of their own. Also, I figured that beam weapons could also be a good crossover option. After all, the main difference between lasers, bLasters, and phasers is aplication (phasers slow and accurate, bLasters fast though less accurate, etc.). Granted, I know that the actual tech behind them may differ quite a bit (I haven't read the tech manuals or any such) but that is less important than you might think.
Some of you may wonder whether this applies "story"-wise. I think it does. Take Star Trek for example (mainly because it is one of the few shows that tried to show adaptation or integration of tech). Many times has the crew of the Enterprise (or Voyager, etc.) encountered a new, previously unknown tech (or a more advanced Version of a known one) and, after analysis, have used this knowledge to upgrade their own weapon systems without changing them (they didn't change their phasers to disruptors, just cranked their phasers).
Please consider this option, I think that it would add a lot to the mod. Though I may just be acting out of selfishness, since I am working on a Borg mod (they currently have a -80 on research and some racial techs that are appropriately lowered in cost) and if they have nothing to assimilate then what is the point?
Joking aside, I do think that this is a good idea. I just hope that I said it coherently. It is very early in the morning...