"Phase skimmer": Wolf and Medusa pay for extra mobility.
In what way? Phase skimmer doesn't cost you any flux at all. While AAF can kill, phase skimmer can save. Plasma jets and plasma burn can allow you to destroy a vulnerable ship, before its allies can retaliate. Fortress Shield and Damper Field can let you survive what should have kill you. All of these let ships do things they wouldn't be able to otherwise. That is the express purpose of ship systems, to let ships do things they can't otherwise. It's impossible to break, abuse or circumvent the rules, if there are no rules, so it's impossible to cheat in this regard. Well, not exactly. Ship systems have no rules, but ships themselves do. They have to pick between defence and offence, they can't attack you without you being able to fight back somehow, stuff like that. There are ships like that in the game, but Hammerhead isn't one of them.
Again, Hammerhead being too strong for its cost is something that can be argued for and that some people will agree with. The insane claim that AAF breaks rules that don't exist doesn't help you convey this point across.
Sucked = was balanced.
Hammerhead was actually harmed by that version of AAF. The enemy could flicker the shield, dodge it, tank it on the shield or be too small to be hit with all the projectiles, whereas Hammerhead had to pay full price in flux for all these shots. It was better not to ever use it, unless you already won, or else the enemy would capitalise on you getting fluxed out. It wasn't fun, it had no utility and it couldn't even do what it was supposed to do (increase the ship's offensive capability). Does this sound desirable to you?
You could theoretically plan for this, by making Hammerhead undergunned, but that would make it only half the ship it's supposed to be every other time. Or you could fire only a few of your guns while using AAF, but good luck making AI do that.