I don't see why the player being able to improve ship performance by understanding how auto fire AI work is a problem. Isn't the point of the game for the player to learn the mechanics of the game and improve their performance? Weapon grouping is a skill the player has to learn: it's just another part of outfitting. You can always improve the AI performance at weapon grouping to make the game more difficult, although I don't think that really a problem right now.
The main reason it's a problem is because the link between "switching weapon groups" and "altering ship behavior" is essentially black magic. There is no intuitive way to understand this and if you can explain it in less than 5 sentences you're probably explaining it wrong. I've been checking out veterans with years of experience, and they still spend hours twiddling with weapon groups because even
they don't know how the AI will respond. They add weapons, remove weapons and play with weapon groups, because those are the player levers to interact with ship AI.
Changing AI with weapon groups is like trying to drive a car with a drum set. You can still drive, but you're driving with a drum set.
Even if you cannot imagine using more than 5 weapon groups, other can. Why say that you don't need 5? Why not any other number? You might be happy with 5, whereas plenty others see the opportunity to use more, so why try to deny it to others?
There was an example of the Onslaught. You can also imagine a Conquest with its two sides. Or Paragon. Or for a non-Capital example, even simply wanting Kinetics, High Explosive, missiles, Ion weapons, beam, PD weapons and an empty weapon group to pilot without bothering to aim weapons on something like an Eagle. It is a restriction, and an unnecessary restriction.
Weapon groups don't solve AI problems. It is also crazy to expect players to solve their AI problems at all, no one expects their player base to be made out of AI designers. If there is a player solution, it needs to be a clear system that provides easily understood AI levers.
Commanding Officers are a good example of a useful player lever. An aggressive officer vs. a cautious officer changes ship behavior in a dramatic way, but it is still easily to understand. So for example if I want my ship to hold back, be conservative with its weapons and stick mostly to using PD, I pick up a cautious officer. If I want a ship to get close, fire ALL its primary weapons and generally run hot on flux, I pick an aggressive officer. That's not a very arcane topic to teach players.