hmmm. The idea of hard flux in the absence of shields is very intriguing. What if right click repaired hull and armor but built hard flux in the process? If you at once free up the "defensive" function of a ship from being a shield to being something else, gameplay can take weird new directions. Phase ships are basically one very well executed thing to be done with this sort of liberty.
Hmm. I always considered repairing armor and hull in combat to be a holy grail. I think this would be insanly difficult to balance out right. an apllied slowdown aoe and speedbuff is the more "playful" option imo.
To be really sure i would have to test both methods ingame. We'll see 
Logistically repairing armor/hull isn't QUITE as powerful with the CR system, so there's that.
How powerful it is depends heavily on the negative effects you attach to it, for example if it turned off your engines, weapons, and built up a huge amount of flux to the point where it's fatal to activate in a bad situation, it's not so great.
You could also attach things like say.. increased damage taken, reduced damage done, reduced range, increased flux buildup on firing weapons...
You could have it deploy a big flare underneath the model of the ship that attracted missiles in a huge range around it to the ship

The nice thing about trying to implement a really powerful concept in a game like Starsector is that there are so many other features you can balance it out with using penalties.
Hell you could even have it lower the
CR of the ship, that would be cool