It seems the easiest way to do that would be to give the standard circumstance bonus of +/-2 for each level of tech above/below your opponent. For weapons, the damage die could change, or become "two handed", or something.
Also, as to feats- I don't think adding some skill-improvement feats would be a bad thing. They're incredibly expensive compared to just buying skill points (since you can get 8+int mod for the same cost as a feat) but they allow you to do better than the max skill rank. A trade off worth considering, so probably an option worth offering.
Skill emphasis (+3), Strong [Military] (+2/+2 to Attack/Defense of any one sort, the variants being Strong Army, Strong Navy, Strong Air Force, Strong Space Force), Industrial power (+2/+2 to any two production skills), Brain Trust (+2/+2 to any two research skills) and so on.
Speaking of skills, I'd think carefully about how you organize the production and research skills. Really, you only need to make one catagory of weapons per combat type (navy, army, air, etc.), if that (since armament technologies apply across the spectrum). Make sure you don't make too many, which is riskier than making too few, I think.
Also, saves: What are they used for?