The problem is, there are not enough (good) modifications to equip to actually make up for the difference. There are basically only 6 good modifications in the whole game of HotAC: Engine Upgrade, Vectored Thrusters, Extra Munitions, Guidance Chips, Experimental Interface, Stealth Device.

I'll disagree here and say that Shield Upgrade is quite good when you have R2-D2 around. So....even if you just took 2 Shield Upgrades, the X-wing would have Integrated Astromech, R2-D2, 3 Hull, and 4 Shield. That's superior to the E-wing right there.

When you look at the Y/K wing, you are really thinking ordnance. So, starting off at PS 6, the K-wing will only get 1 Modification. Which is it? Is it Guidance Chip or Extra Munitions? It can't have both to start off with and has to get to PS 8 to get the 2nd. So, you are only really going to be able to use a maxed out K-wing at the very end of the campaign. In the meantime, the Y-wing at PS 6 will have GC and EM, as well as 1 more Mod. Let's say that 1 Shield Upgrade or even Vectored Thrusters. So, I consider them pretty equal at that point.

Still not convinced that a 3/2/3/4 X-Wing with R2-D2 is superior to the 3/3/2/3 E-Wing with R2-D2. The E-wing takes less damage in the first place and I think 3 shield to replenish is almost as good as 4 shield to replenish, considering you need 3 or 4 rounds to refill that (face it, you won't go 3 rounds without being attack so you won't need more than 3 shield value, at least not for R2-D2 to be more efficient), plus the E-Wing has the better dial to recuperate shields because more greens. The E-Wing then also has Barrel Roll and Evade Action which the X-Wing does not, so it can dodge arcs better to evade the attacks altogether and no need to recuperate shields.

What I found so far is that regen is not worth it in HotAC (your campaigns might differ? I don't know), since usually damage gets piled on in an amount that you can't recuperate with R2-D2 but instead only by evading shots and killing TIEs before they shoot. It may come down to how many players play? We had pretty filled here usually, so there's many TIEs and the nearest pilots get showered in attacks, so an E-Wing with Sensor Jammers and 3 AGI beats the X-Wing any day.

Also with the K-Wing, easy choice, even at PS6 with only 1 mod the K-Wing carries more weaponry than an extra munitions Y-Wing. So I already have more ordnance with me to fire before I have to use my turret, can safely choose guidance chips and have the same attack power as a Y-Wing on the ordnance, (one torpedo less though) and in addition 2 more bombs (or 3 with additional bomb damage when I bring Sabine). So out of the gate on PS6 I have 3 GC missiles + 3 power bombs on the K, without extra munitions, the Y can only bring 4 GC Torpedoes or 2 GC Torps/2Bombs, and the bombs will be weaker cause no sabine on it. And as I said, the additional slot on the Y-Wing with Shield upgrade only brings it to the total hp of the K-wing so only draws even in that. Vectored thrusters may be a good addition but only if you don't go for Nera Dantels' pilot ability, so you have to actually fire your ordnance in arc. If you use Nera Dantels you have no need to reposition since you have turret-torpedoes/missiles and when they're out you have your turret.

Agree to disagree?

Still not convinced that a 3/2/3/4 X-Wing with R2-D2 is superior to the 3/3/2/3 E-Wing with R2-D2....

Also with the K-Wing, easy choice, even at PS6 with only 1 mod the K-Wing carries more weaponry than an extra munitions Y-Wing. So I already have more ordnance with me to fire before I have to use my turret, can safely choose guidance chips and have the same attack power as a Y-Wing on the ordnance, (one torpedo less though) and in addition 2 more bombs (or 3 with additional bomb damage when I bring Sabine). So out of the gate on PS6 I have 3 GC missiles + 3 power bombs on the K, without extra munitions, the Y can only bring 4 GC Torpedoes or 2 GC Torps/2Bombs, and the bombs will be weaker cause no sabine on it. And as I said, the additional slot on the Y-Wing with Shield upgrade only brings it to the total hp of the K-wing so only draws even in that. Vectored thrusters may be a good addition but only if you don't go for Nera Dantels' pilot ability, so you have to actually fire your ordnance in arc. If you use Nera Dantels you have no need to reposition since you have turret-torpedoes/missiles and when they're out you have your turret.

Agree to disagree?

I'll agree to disagree, but I think the X-wing can be close to the E-wing with 2 more Modifications. If you don't rate a lot more shield, it's easy enough to throw on Vectored Thrusters and/or Engine Upgrade. I think that can make the difference.

As for the Y-wing I get a little confused. The K-wing w/ GC only has 2 Torps and 1 Missile while the Y-wing has 4 Torps. Yes, the K-wing has 2 Bombs, but I just don't rate them the same as either a Torpedo or a Missile. That's just my mileage, though. So to me, I think the Y-wing has the advantage, even if just a slight bit if you consider 1 Torp > 2 Bombs. I will say, though, that the K-wing will still even have to buy the Bombs and Missiles. The Y might have had Bombs earlier, but not Missiles. So, it would still require a bigger investment to get a Crew, Missile, and potentially Bombs (I never get Bombs for my Y-wing).

I do think there is a reason to take Vectored Thrusters if you have Nera's ability. It's still nice to get out of some firing arcs, dodge some terrain, set up for next turn, or even just edge a little closer/further to ensure the shot you want is in range 2-3.

Personally, I still think E-wings and K-wings shouldn't be used in the campaign, but if you have people that are really dead set on using them, I'd push to use the rules with -2 Mod slots over not having that rule. It might be that the E-wing and/or K-wing is still just a little bit better, but at least it's a lot closer.