I find the Borg regen ability is to strong when you add it up with all the other things they are strong at. They hit super hard, they have really high armor, and (at least the lower ships) can enter their hibernation mode and regen HP at 45 a second. I think some have even higher regen. This does make sense for the Borg but the problem is, in the early game you can't kill their ships because you need to reach a certain "critical mass" before you out DPS their regen. When I fight the Borg I feel like I'm either unable to touch them, or I've reached a state where I can overwhelm them with shier numbers. Theres no middle ground where your both equal.
Also, I find their early colony expansion is to high, even for the Borg. In a game I just recently played the Borg had 6 planets colonized 2 minutes into the game. I do think that the Borg should be fast expanding and self regening but I just think a lot of these stats are just to high currently.
I also have a question. Are the Borg getting some form of shield mitigation even though they don't have shields in the game? Maybe its just the high armor thats making me think that.
Regarding what you posted about an anti-Borg research tree, I think thats an interesting idea. You could also include that type of research in the current research tabs depending on what category it falls under. It would also let you put higher level skills more naturally further up the "tree" intermingled with all the other research.
Also, for what you said about a transport ship for hauling goods around. Its been shown in several of the shows that civilian ships are often used for this and theres lots of different ships shown over the years hauling cargo. The civ cargo ship shown in Enterprise is similar to the one in Armada and it would make sense that the overall design wouldn't change all that much over the years. (A truck is a truck.)
BTW if theres a model you do need made you can let me know. I haven't done a lot of modelling lately but I should be able to make whatever you need. 3D modelling for games is what I took in college.
Just let me know, I'd enjoy making something for this mod. 
Edit: Maybe use the long one like the one from Armada for "goods" and use one of the Antares varients for "ores"?