My opinion: I hate armor upgrades, and I think they ruin the game, completely and utterly.
The Facts: Armor upgrades are essential to the balance of the discovery universe due to bombers and capital ships. They are also a precious few of the customizations you can do to your fighter.
My suggestion: Increase the hull damage of hull based fighter weapons by 10%. No more, no less. The 10% extra hull damage across the board on all hull weapons will help to counter-act the multiplied armor without severely unbalancing the entire mod, it will also decrease the duration of fighter vs fighter combat without making it 15 second fights.
Just my opinion as I think it's the best way to balance it, even though my opinion would be to remove them completely.
As it is now, I see more bombers than I do fighters. Why? because people need the SNAC to keep their engagements from being 20 minutes long due to armor upgrades. (That and caps, but bombers shouldn't be useful against a fighter at all IMO, but that's another discussion)
edit
Just a couple side notes, this would also mean that light, and heavy fighters would have a little bit more of a punch against fighters and bombers, which is a VERY good thing.