Nothing says AA weapons have to be short ranged. Like I said above, a Range 9 4+ 3/1/1 weapon makes a nice general purpose weapon and isnt that expensive to field. A handful on assorted ships and you are generally pretty well protected against all but the largest Fighter swarms.
As far as Fighters not halving shields, I still think you'd have to reduce their cost accordingly or they are not worth it. 50-60CR is pretty steep for effectively an R:1 6/1/1 that is extremely vulnerable to return fire. That is 50-60 RAW CR. Almost no weapon that is that weak will add that much CR to a ship. As an example, take the following:
A Size 6, Speed 9 Shield 4 ship. Create a weapon that is R:3, 5+ 3/1/1. That weapon's base SU is only 4(!). OK, you can mount 15 of them forward firing on that ship (AB arc) That 45(!!) dice to attack and they are more accurate than Fighters at R1 (because Fighters hit on 5-6, these are going to hit 4+ at that range). The ship's CR is 123, or about the equivalent of 2-3 Squadrons of Fighters.....Obviously the Fighters are a little more versatile in that they dont have to plot their movement and can guarantee getting the first shot etc, but that ship is still getting almost 4 times the firepower with the same speed and probably more survivability (although that depends on the enemy weapons).
That said, I see Fighters as one of the potential screws to any battle. If someone brings enough of them to the battle and you HAVENT set yourself up to deal with massed Fighters, you can pretty much say good night. So, to me it behooves the players to make sure that the game isnt always played double blind when it comes to enemy forces. People should have a reasonable idea of what they are going to face to prevent 'gotchas'.
There are a number of such 'gotchas' that are possible but massed Fighters are the easiest one to pull off without seeming like a complete cheese monkey. 
Because as I said above, Fighters act a force multiplier amongst themselves. The more that are brought, the more powerful the 'alpha strike' and consequently, the less return fire they have to endure.
I would also mention that when trying to determine what WAS optimized in the game, we identified Inverted Range, Repeaters as a bit over the top for a 'fun' battle, especially if its base to-hit is 3+. At LR, it makes the hit number 2+ and with repeating, it leads to about 5.5 hits per shot (and in the case of your wife's weapon x3 for RoF = about 17 hits, x2 for Pen = about 34 Pen dice..even when fired at a shield 5 ship, that leave 5-6 to penetrate the shields and then with a 2 Dmg, thats between 10-12 damage on average) Keep in mind that that is against the largest shield factor possible. Having any lesser shields means you are likely to be incinerated in one shot. The No-Hull Damage brings the cost down considerably, but that much damage still reduces most ships to empty hulks in a round or so.
So, my bet is that she could win most games with that weaponry loadout without regard to the Fighters. Its just way too unpleasant for a 'fun' game IMO. Repeating is the only weapon without a damage cap...it can generate effectively unlimited damage on good rolls. Nothing else comes close in terms of potential damage curve. (I have a friend who graphs such things out for fun and its an eye-opener sometimes to see the results).
If you want a fun companion weapon, go with a R6 or R9 3+ 3/2/1 Range Based RoF and/or Range based Dmg/Pen and Double Range mods. It will be reasonably cheap and will again annihilate anything that comes close. So, you have your choice of staying at range and being pounded by the repeater or closing in and dying even faster to the range-based weaponry.
A lot also depends on what Optional rules you are using. We quickly found that the Emergency Thrust rule makes short-ranged weapons devastating. You can quickly negate a range advantage and if your ships are loaded with a preponderance of Range-based weaponry, you can pour out sick amounts of damage in single round.
The game provides a great framework for setting up battles. But to me, its really necessary to have the opposing ships designed to be more 'fun' than optimized. Its something my group has a hard time with, but the experiments with 'anything goes' have led to games that were basically won and lost before ever beginning. Sun Tzu states that every battle is won before its ever fought, but that doesnt lead to a very fun game.
Be that as it may, the system is definately flexible enough to allow for house rule changes such as what you propose for Fighters. For me, I think the current Fighter rules (with a few cost tweaks) are fine as long as the game itself is 'policed' to make sure that its going to be fun for both sides.
Please post how your Fighter changes work out in practice.
