As AI ships are my fav ones I have to say like Histidine mentioned, you really need to keep at least some guns deactivated. What kills the flux usually are fighters, cause they make all my weapons go off. I keep active at all times the point defenses (which I decided to just use long range PD lasers cause the AI PDs seemed to miss a lot the faster fighters and missiles and were wasting flux) and the shield penetrating weapons I have. When it is smaller ships I do not bother to turn on explosive weapons at all, even if their shield fall down. I just blast them away with my frontal awesome lasers. If the enemy ship is large, I turn on the explosive weapons , to help myself take him down faster. Of course as soon as his shields are up, I turn off the explosive weapons again.
I do not know if you realize it, but that Capital is overpowered by a lot. It can plung in the middle of battles without shield on and it will still destroy everything, with only minus being that it needs to vent after every enemy or a couple of times on bigger ones. If it had any more flux, which would make venting less of an issues, it would be even more OP.
It is like giving Thor a higher armor and more flux. >.> OP things should not get more OP...