Having the option to mount something else, than the armor ugrapde is a good idea. We could take a step forward and also add shield upgrades, mass reduction kits and so on.
Now, the main problem is, the armor upgrade is a too much of a must.
Let's take an eagle for example. Base armor is 9900 (Finally!). If I buy one, I have to decide: Do I want to have a bit more energy or 2,5x armor. I think nobody would go for the energy advantage (maybe 1 or 2 masochistic players). Nukes and razors would instakill VHFs (no matter how much of an ace one is, everybody gets a razor in the face time to time). 2 shots of a guardian with full 2.00 would also instakill most of the fighters.
Say, if the ships would start off with 2x more hull, than now (in this case the eagle would have 18800 hitpoints by default), and the armor upgrade would only give you +25% armor or so, then things like powercore upgrades, shield upgrades, mass reduction kits etc. would actually become useful.