Put points into subsystem repair, and run as many human boffs as possible. System downtime will only be a few seconds. Engineering team will also remedy this. It is hardly a huge drawback, as a focused science build can now concentrate solely on Aux power without worrying about a drop in damage.
It is working as intended, in fact the game was patched to add it.
Knocking weapons offline takes out aux cannons as well, so that you don't get around skills like TSS:W.
IMO Aux cannons aren't that great anyway, so who cares.
They should not be tied to two subsystems. You say that they would get around TSS:W but they fall victim to TSS:Aux. Let's face it, Aux is the skill that a sci dreads losing, so taking the Vesta's weapons off line for losing weapons really blows.
Who cares? I'd say people like me who use the Vesta with aux cannons with max aux power and no weapons power.
I thought they patched it so that Aux cannons are only disabled when Aux is disabled. Did they unpatch it recently or something?
"Don't let them promote you. Don't let them transfer you. Don't let them do anything that takes you off the bridge of that ship, because while you're there... you can make a difference." - James T. Kirk
Well, the devs say you are wrong, as they used to work they way you say and they purposely changed it to work how it does now.
It is how it works, and if you are using aux cannons that is a situation you have to deal with.
I don't use the aux cannons on my Vesta. There is a reason. You're half way there already.
Next you will notice that as you fire with your aux cannons, your aux goes up and down, so your sci abilities lose consistancy.
Then you realize that you still need weapon power anyway, or else your turrets and such are gimp. So you are still trying to maximize both power systems like any other non torp sci. You realize you aren't really gaining anything, just shifting the burden around.
Then you realize that there are better phaser cannons, and so for all the hassle you were dealing with to break even, you are then behind because the weapon itself is inferior.
Yeah... I could be arsed what happens to aux cannons, I replaced that starter gear ages ago.
Edit: I don't know if maybe they made a new patch to the old patch that I missed, but no, the last time I was aware they patched the cannons from being aux only. Originally you could fire them under the effects of target sub systems or one of those tholian torps or what have you. They nerfed that right quick because of course you then just load an aux and a normal cannon and your weapons never go down... which is the behavior the OP wishes they had. It was nerfed for being herp derp overpowered.
Purple text that says mkxii doesn't make good endgame gear.
Stats make good endgame gear.
Aux cannons aren't terribad, don't get me wrong. I'm not saying you're a gimp if you run them, they perform adequately.
Min maxing it is damn near impossible to get them to break even with even regular DCH with the same stats, let alone one with better mods.
Edit: Hell, using one is even a benefit in certain circumstances. So much of a benefit that it was nerfed down for being overpowered, but the OP would like that old functionality restored. I could be arsed one way or the other to be honest, just dropping the memo off not to expect the change he desired, and some ways of looking at it to soften the blow.