1. Fighters are very non-cost-efficient. Fighter bay takes 40 space, and hosts 5 fighters. It means that one fighter takes 4 spaces. It's comparable with one light gun... but I can make a scout with 6 such guns. And I can make one scout every single turn in the every single planet of system - unlike ships with fighter bays. So scout is better fighter than fighter here. Consideration: make fighter bays smaller, or make more fighters in the same bay. Maybe both, during technological progressing.
2. One scout can make up to 6 shots, destroying or damaging 6 different targets. All 5 fighters are shoot at once, hitting exactly one target per turn. So very purpose of real fighters: counter enemy fighters, annoy bigger ships and destroy missiles - does not work at all. Scout is much more effective fighter again. Consideration: give squadron guns the same individual targeting as all other ships have.
3. Scout can be quite hard with regenerating armor, invisibility, shields, etc. Fighter is one-hit-one-dead issue. Yes, they are small, but taking that they cannot be too numerous for ones, and cannot harm anyone too hard for second, being too easy target makes it useless at all. Consideration: use the best possible armor+shields for fighters. Alternatively, make fighters non-targetable for a bigger guns (something like reversal of planet attack will work, I suppose - only light/lasers/smaller guns can target fighters). It will make fighters more annoying, at least.
