In this mod, missile and torpedo armaments in space do not bypass shielding, a near anomaly in the Empire at War community. (A notable exception would be vanilla's diamond-boron missiles.) However, I have come to realize why this is so: it would make fighters way too imbalanced.
No, they tend to not do it out of a combination of not making a change they think is unnecessary, and people think that missiles bypassing shield is canon. On what basis is this unbalanced? When bombers could bypass shields, it just meant bomber swarms could nuke any ship with no recourse and didn't have to worry about shields at all.
On what basis is this change a buff instead of a huge nerf? You even acknowledge that this is a nerf later in your post, so I'm confused as to what you're actually arguing here.
Think about it. TR fighters have these advantages over their counterparts in the parent game and other mods:
Almost every fighter carries a projectile weapon. For example, the Republic not only has torpedo-carrying Y-Wings but two effective fighter-bombers (B-Wing and X-Wing) and the missile-armed A-Wing.
You're comparing things as if the properties and relative strengths are the same, which they in fact are not. Missiles and torpedos don't do the same thing in the mod; their flat damage isn't the same, theiur recharge rates aren't the same, and they can't bypass shields, which makes them way less effective against larger ships. The recharge rates in particular are very important, and you seem to have completely disregarded that. You can't say the x-Wing is on par with the B-Wing or any other bomber when they get a single proton torpedo every thirty seconds. If they could bypass shields it would add up because the hardpoints don't regenerate, but with that firing rate most ships would be able to regenerate past it; it's almost negligible unless you're backing it up with some way heavier stuff. You can't just say "this has proton torpedos in the base game and this has proton torpedos in the mod so THEY MUST BE THE SAME THING"
They come in squads of twelve, as opposed to the 3-5 per squadron elsewhere, meaning better firepower and a longer lifespan.
Again, not necessarily; you need to look at the entirety of the changes and not just compare them on single lines which would make them more powerful. If we had just taken the base stats from the vanilla game and multiplied the number of fighters by 4, then yeah, that would be more powerful. We didn't though. In vanilla, fighters could tank multiple shots from both other fighters and from larger ships. In the mod their health is far lower, so their lifespan is in fact way shorter. You can take an individual fighter out with one shot. And again, you can't compare a single projectile from us to a single projectile from EaW. Fighters do proportionally less damage, once again. Also, I'm pretty sure this is a change almost every single other major mod has made.
They are launched in huge quantities; a decent-sized carrier can have five or six squadrons. And the main reason this is being changed to a standard active/reserve capacity is not for balance, apparently, but for performance.
If you'd actually read what we've said about this, it's being done for both (and a third reason which I'll get to). However, although fighter spam was still one of the most effective tactis, it's still way less effective than it was it was in the base game. Yes, carriers gave a different avenue for this to be done, but the tactic itself was still more powerful in the base game because fighter squadrons were
proportionally more powerful in EaW than in ICW. In EaW if you build a full fleet of X-Wings and Y-Wings as the Rebels, you could beat almost anything as long as you brought one or two Assault Frigates to beat the one or two possible Tartans (which couldn't actually beat that many X-Wings) especially when projectiles could bypass shields. In the mod, if you did the same thing and filled your fleet cap with fighters, you'd lose.
We've highlighted the performance reasons for the staggering over the balancing reasons because I think they're the most impactful of the two, since fighter spam as a tactic is nowhere near as problematic as it was in the basegame, whereas the number of fighters (especially of specific kinds where the models are older and less optimized)
was the main cause of poor performance for most people who experienced it. The other aspect to this change was the fact that
any fighters were having problems surviving until the end of the battle and we wanted to make sure there were at least some left by the end of a game.
Frankly, all you've done is say "there's more of them so they MUST be more powerful" but you haven't actually given a basis for this, and extrapolated from data that isn't actually true. While there are more of them in the mod than in the base game, they're also far weaker and the spamming tactics from EaW that centred around building them no longer work anywhere near as consistently.