If you truly believed in the whole "if unit 1 and unit 2 do the same thing, they should have different counters" BS, then you should think that carriers shouldnt counter all 3 fleet heavy hitters (LRF, HC, Capital Ships).
Carriers counter nothing. Fighters
counter LRF and Bombers
counter HC and Cap. Ships. Depending on the enemy you will face, you must change units to suit the situation - building carriers will not save you if you don't equip them properly - it's about making tatical decisions so you are properly equiped to counter the enemy. The only time when a carrier could technically counter everything would be a Sova using RM, in which case it would have instant access to fighters and bombers, but that's beside the point.
Consider the defenders burden in a situation where assault cruisers are countered by Bombers. You can only have so many strikecraft from defensive structures, being forced to divide them in half to go half bombers, half fighters would make them all over useless against fleets with many many more SC than a planets defenses could hope to handle.
A defender should have his own fleet backing up his defensive structures. As many have said, these structures mearly serve as a means to buy time for your own fleet to tackle the enemy, they are not the be all and end all of Imperial Defence. The primary purpose of defensive structures is to give your fleet and advantage in your own territory (Repair, Fighter cover, etc.) not fight the enemy for you. If that were the case, empires would be impenetrable.
All the defender needs to do currently is a bit of fighter micromanagement and the assualt cruisers are toast. He is at no disadvantage from sitting on his rear and letting the enemy come after him. If he has his own fleet in the well (as he should) those assualt cruisers are toast from fleet FF and large groups of effective counters (Fighters) focusing on them, no matter how many flak you have. If assault cruisers are less vunerable to fighters, then by building them you actually nullify one of the advantages the opponent has against you, and if the opponent has to build bombers to counter the assault cruisers, he has to make a tactical choice; "Do I build bombers, and risk getting caught with no SC cover, and hope he is slow on the assault, or do I stick with fighters to protect my fleet from enemy bombers, and hope that my fleet can take out the assault cruisers?" Tell me, is that sort of situation not the essence of strategy games?
And if you have been the ingenious person who has built lots of flak to kill off the enemy fighters, please tell me how you will counter the fleet in the gravwell with your autocannon army? Flak are (comparetively) rubbish against anything but SC. You go with a fleet full of Flak and AC, the enemy fleet will clean you up, considering it should be there supporting the defensive structures. If it isn't, lucky you, you probably won six planets ago anyway; you know, when you wiped out his fleet and this is just mopping up a stubborn player, or something?
Fighters and Bombers get the same modifier to heavy armor (50%). That doesnt help if you want bombers to be the answer.
Well perhaps give them V-Heavy armour then. It doesn't change the fact that the game's two structure busters are vunerable to the same thing.
Pretty much ANYTHING except certain structures counter them.
Aside from the obvious question of which structures (and don't say hangar bays, for the reasons mentioned above) note the conspicuous lack of the word "effectively" in this sentance. The issue is not so much how
I can get rid of the assault cruisers as how quickly
I can get rid of the
assault cruisers before they eat all my structures. With them using light armour, the advantages for the opponent are minimal, as hostile fighters can mince them before they do too much damage, just like with the bombers, but with heavy(er) armour, those fighters are a far less of an effective counter, and so the opponent's assualt cruisers can cause more damage before they are destroyed (or pulled back) making them a much more effective choice to fight a fighter heavy enemy. Said enemy is forced to make a tactical decision, to try and fight you off with what he has, or change strategies in an attempt to out-manouver you. Currently, he doesn't have to be fussed either way, as he knows no matter what is coming, he has an effective
counter to your attack. Counters are far more complex than what unit X can or can't shoot.
So, I suggest we add "Change assault cruiser armour type to be less vunerable to fighters?" up there, and see what the public thinks.