Target painting would be interesting, but it would make it very hard to hit anything.

Torpdoes need to be balanced so you only get one chance at a hit. If a fighter is almost directly in front of you, you should hit. However, once it doges, your torp won't be able to turn quickly enough to catch up. Torps should primarily be for attacking capships/transports. They need a 30 second lifespan for long range atatcks.

Missiles need to be given a long locking time than they do now, say 4 seconds. Then they should be fire and forget. They need to be accurate, yet have a limited lifepsan (15 seconds). That makes them dodgeable by faster ships, but it takes skill.

A major problem that came up in a mod for a diferent game (anyone played Freelancer?) was Imperial/Rebel balance. You can either give the Imp fighters shields and missiles, or make them incredibly fast and agile, but only have lasers (except for the Bomber obviously). If you go with the latter, this makes piloting either side's ships a totally different experience. However, in this case, you need to give X-Wings missiles to balance out with the TIE Fighters. I'll post this in a table to stop confusing everyone. My diea of a balnce system, basically:

Imps     Ability

T/F        Agile/2 Lasers
T/B        2x torp load of Y-Wing
T/I        Fast/4 Lasers

Rebs

X-Wing   Missiles/Shields/4 lasers
Y-Wing    Shields/Gunner
A-Wing   Fast/shields/2 lasers/missiles/weak hull
B-Wing   1.5X torp load of Y-Wing/shields