They could introduce the rules in a Avenger Squadron and Gold Squadron two pack called "Legends of the Civil War." The squadron ability only works if every ship in your fleet is in the same Squadron, including named pilots.
Just acouple examples off the top of my head.
Saber Squadron can change any forward manuver to a white 1 forward movement.
Alpha Squadron gets a missile for free.
Avenger Squadron (Interceptor) Is allowed four modifications total or a combo of 1 system, 1 cannon, 1 missile, 1 bomb, 1 torpedo, 1 beam the equals up to four add-ons.
Avenger Squadron (Avenger) is allowed the same as the Interceptor version except its 2 with no missile and no beam.
So far Avenger would be the only squadron to have mixed ships with no added cost.
Royal Guard Interceptor could get some extra bonus for when Darth Sidious is on the table. Maybe one of their dice attacks is not effected by defensive actions.
Gold Squadron gets A4 Ys with stregnths 4 attack, no turret ,two less shields, 2 more hull and a bomb option in exchange for torpedo (optional) and X-Wing dial
Gray Squadron Gets S3 Ys with crew spot, two more shields, two less hull.
Rogue Squadron gets three mods.
These are just examples and they can be changed. Please put your own ideas here for the squadrons listed and for the ones not mentioned.
In addition to all of this some squadrons, groups, and Wings have mixed fighters. Avengers is the only one not charged for having a mixed force. Every other organization pays a half point for converting un-named fighters too their organization. So you can have a dagger converted to Gold along with one Rookiee and one Red X-Wing and one prototype A-Wing for 2 points total minus ship cost.