I guess the reason why i am opposed to the idea of having the ability to repair armor/hull is, its a bit "boring"
Wait...I think I get it. Modders need to be the one to get the most out of thier own mods. I get it that you want something to change and you want a little more zing and challenge in your own faction. You've been really polite and open minded to receive all our opinions on the matter even though in the end you want
something to change. In that way it's possible to make a compromise. Your argument about keeping in the mechanic about flux build up makes sense. If you wanna add shields, how bout using the shields as a means to repair. Meaning that, your can't repair unless your shields are up and having them raised means to build up flux. If you're getting bombarded than it will be a gamble....will i be able to repair in time?, will my shield collapse and leave me a sitting duck? or even if i do repair in time ill still have to vent all this flux. This way repair in battle can only in the most optimal situations, is when the ship in question is not being attacked or near the battle.
It could even be set up as the rune ship power. When activated, cut power auto raises shields, repairs are made. If duration of time passes, without shields breaking, repairs are applied. If shields are broken before the time frame, repairs fail, sitting duck time. Also add a cooldown after the power is used.
Now you have something that works, is unique, and requires thinking on when and where to use.