EMP and flux work similarly for me, yes, but I think it would interesting to have two methods to achieve a similar goal. I just want to make it so that taking hull and subsystem damage isn't the only thing you're afraid of when engaging the enemy. Like in normal Starfarer with shielded ships, you have to keep an eye on your flux levels in combat. I'd like to do the same in TA. At the moment, flux is only used for determining how much you can fire your weapons--which is about all it is used for if a ship doesn't have shields.
The way I see it, the main problem with flux and EMP is that I can edit the amount of flux that ships have (both ingame and out-of game), but I can't edit the amount they receive from weapons--and I can't edit the amount of health a ship's weapons have (Outside of a universally used hullmod, that is), but I can edit how much they receive from weapons. As you see, both systems really only have one variable I can tweak. If both variables were open to editing on either system, then it would work excellently for me. I remember you saying sometime in the past that you would eventually make it so the health of individual weapons could be edited, so that right there would solve the problem.