You can edit the .tweak files for both gunships... to compesate for any advantages you think one has over the other. For example, occassionally the PAC gunship missles will not track on the EU gunship at all, due to the mentioned bug in the EU hitbox mesh... the hitbox not registering at all (temporarily for a 15-25 seconds in the game, at random occasionally)... so what I did, was make the radius for the PAC missles to detect the EU gunship a bit *BIGGER*.
So what happens is the PAC gunship has an advantage over the EU gunship most of the time, to a semi degree... missles shot at the EU gunship will swerve toward it further out than against the PAC... under normal dogfights... and then when the PAC missles 'fail' so to speak for a short duration due to being mass produced in China so to speak in bulk... the tides turn slightly, you have hit point blank on target BF2 style with the PAC gunship missles, and the EU gunship has its moment in the sun. I mean, you know how to aim, right? Seat jump, use the TV guided missle, and take the EU gunship out with one shot, or just flip your shields on and land on his head briefly, that will kill him.
In the end, it all balances out in the game. I can post my PAC gunship tweaked code here, but I'd have to dig it up... the mod is not hard to make, all you have to do is unzip an archive, edit one line in one text file, and rezip the archive.
Me, personally, I don't bellyache about any weapon having flaws against any other weapon... you use what's in your hand no matter what. To whine that this is better than that, etc, is just weakness. A warrior can kill a guy with a machine gun with a fist full of sand...