The only complaints I have about wingmen AI on Prophecy are true in all WC games-
The Friendly Fire Scenario-
You're in deep **** if you get between them and whatever they are shooting at because they don't stop firing after they hit the first or second time, they just keep unloading his/her gun battery until you die or happen to get out of the way (which is obnoxious considering if you accidently shoot them once, they whine and moan like no one's business)
The Single-Mindedness Scenario-
WC wingmen often tend to fixate on one target, even at the expense of the mission- "Let's all focus on chasing that one light fighter around while three or four heavies are pounding our carrier/transport/bombers into dust!"
The Wing Management Scenario-
This kind of plays off the previous scenario, and is more of an interface issue then an AI issue, but it drives me nuts how hard it is to arrange for your wing to do any task that requires a division of an element consisting of several fighters- for instance, you can tell all of them to "Attack my Target," but you have to individually target your wingmen, comm them, and then target a specific target if you want to divide your wing in half- for instance, if you want to tell your wing of 3 to each engage seperate enemy ships. They also don't have any mission specific commands- e.g. I can't tell them to "Escort Transport" so they focus only on ships making runs on the transport instead of chasing around space superiority fighters without specifically finding out which enemy targets are targeting the transports myself, manually comming and designating the targets to each wingman, and trying my best in the meantime to do my part as a mission element to ensure mission sucess. I guess, in summary, I wish for easier wing commands!
Really though, independent of the above, I like the Vision AI. On Nightmare, the fighters behave according to their strengths, especially in Standoff- I can't count how many times I've been toasted by a light fighter that slid around behind me and shoved a DF up my tailpipe, or a Drakhri (spelling?) that just unloaded it's guns. The only things I would change (if possible) would be the frequency enemy fighters use missiles (I would make them use their missile loadouts like they were going out of style, which would make the missions wayyy harder, but more realistic (relatively speaking)) and program enemy ships to occasionally try pulling tried and true WC manuevers, be it the Shelton slide, using autoslide to turn around and blast backwards, sit n' spin, hard brake, etc. Having enemy pilots act in tandem would be kind of cool too (for instance, having one attempt to drive the player into the gunsights of another), but that's asking too much.