armies are always fighting the last war. survivors come home with scars and lessons learned and ranks achieved by virtue only of being still standing at the end, and busily begin the process of figuring out what they should have done to keep more of their friends alive. but everything's obvious in retrospect, and the enemy learns too.
R&D is always fighting the next war. or trying to make war obsolete. or working on something completely unrelated that just also turns out to be able to fly or float or explode or reduce humans to paste or circuits to scrap… if it actually works on the battlefield.
fighting the last war makes you predictable. trying to fight the next war needs you to be lucky. it was the bureaucrats who forced the compromise that is modern pilot hardware, yoking the fractious generals and scientists together in the present.
the original, basic function of the implants is keep our pilots alive and conscious through high G and EMP and blood loss and battlefield fatigue, and to keep them informed and connected to the network. the implants work very well. the technology matured a long time ago.
but they can only help so much if the pilot's training is wrong: if she has learned to duck under an incoming K-29b, and then the K-29c comes along with better lookdown sensors, well, that's all over but for the flag they mail home.
so the other function of the implants, sacrosanct, in place of all the other features that the lab monkeys claim they could be fitting in that limited space instead, is memory patching. faster than training an old reflex out of someone and a new reflex in. click. download. done. keeps you fighting the current war, and winning.
don't worry too much about how. the side effects from a few too many doses of neural plasticizer is a small price to pay compared to death, disability, or forced retirement. besides, they don't mess with the higher functions much: principles, ethics, loyalty, if you had any to start with, you'll probably still have them. those are much less amenable to memory patching than the low-level functions. muscle memory. threat recognition. fight/flight balance.
it's true that there are some side effects that can be more initially distressing than others. they're fast low-level reflex functions too, and the patch source could be anyone in the fleet, after all. broad compatibility is important. so yes, sexual preferences and orientation can get a little… blurry. but you'll get used to it, pilots. the system works. □