As nano armor and bio armor. That is, change reactive armor to nano armor, and give it slight resistance to missiles when BE researches it. Also give comp armor slight resistance to cannon fire when researched by NF. This would actually be fashioned by making 4 new armors, 1 be and 1 nf variant of each, then making 4 different researches and have each be team specific and point to the specific armor. Just an idea that I threw out in IRC and thought I'd share it to a broader audience.
what? Electrical Engineering would have nano armor (regnerates). The armor would have a slightly different effect for be (presumably better effect) than it would for NF as the BE are more proficient with nano tech. NF would have bio still, but it would receive an equal and opposite buff for nf being more proficient with biological enhancements.
so basically you want to make it so NF always researches bio armor, and BE always researches "nano" armor i hate "lets make this better for this faction" ideas in theory its kewl, untill you end up with both teams only using those armors that are beter
One armor would have slightly better resists towards missiles and one slightly better resists towards cannons, but balance it with regen time or something. idea is to make the armor stronger in a straight up point blank blast away, while not losing some of it's innate abilities in exchange.