Scipio:
In response to your thoughts, this was some of the reasoning behind what I choose...
The Federation would not have relatively good ground troops - overall the Federation is non-combative and their experience would be less than other races that have fought frequent wars. This is also the same reasoning behind the ship defense and attack bonuses. Did you ever see the Federation ships dropping like flies in many DS9 battles? Plus, if we based the Federation exclusively on what we saw in Star Trek - we'd have to give them bonuses in everything and that would be a balance issue against the other races.
The Klingons have a distaste for science and hence why there research is low. Keep in mind also that the Klingons have been in space much longer than the Federation, but have advanced at a much slower rate. The production bonus is appropriate to the warrior race motif, and really doesn't make much difference anyways. The Klingons do enjoy some good combat bonuses which during early testing did help in battle.
The Romulan shipyard rate was set lower because they spend a lot of resources building oversized Warbirds that have a seemingly poor combat record for what you'd expect them to do. The Romulans are also portrayed as rather secretive and isolationist, so why would they be out and about trading so much? The honorable demeanor could be changed, but Romulans hold honor in more an individual patroitic sort of way.
The Dominion didn't really trade in the Gamma Quadrant...it was more like extortion. The increase in shipyard rate would help pump out more smaller attack ships, but wouldn't really make a difference with big ships due to their high cost.
I suppose the points about Cardassians are somewhat valid, but then again the Cardassians are a much more militaristic culture and it would seem reasonable to believe that they are better trained in combat situations than the typical starfleet officer. I gave them +5 for intelligence since they seemed quite renowned for it and plus, they needed a bit of a bonus somewhere else.
Remember, not all spying is done undercover...don't you remember Quark - seemed he knew lots about everything - Ferengi deal in information a lot you know!
The Borg can and do research - although it's true that most of the stuff they get is assimilated. Being truthful, you could give the Borg culture bonuses for almost everything if you think about it. I believe the shield depleter and tractor beam are different, and anyways you couldn't assign a se4 weapon with both those abilities anyway.