I love me the pistols and would play AoMr games before it was actually a challenge. However, it takes 3 traits to make pistols worth starting to use after you find your first Combat Shottie (SoaG 2 + Dual), then a 4th (SoaG 3) to stay useful later on. This is a heavy investment that someone using other weapons could have used to get +30 HP and +1 armor or to have started on Eagle Eye for Chain Gunning or for Son of a Bitch or ...
Now, your argument against all the other weapons can be more than fixed by traits. Pistols take more traits than any other weapon to be good. I'd put it at at least 6, more if you don't have artifact pistols or a lot of damage mods. 2d4 damage against armor starts to become *pathetic*.
A plasma gunner with EE 3 and SoaB 3 vs a Pistol user with 6 traits (SoaG 3, Dual, EE 2). They have, at that point, similar accuracy (Pistol has 1 higher), the pistol user can get out 6 shots in the same time as 8 shots from the plasma gun, and deals an average of 5 damage per shot compared to 7.5 with the plasma gun. Against something with 1 armorthis is 4*6 = 24 vs 6.5*8 = 52; with 2 armor this is 3*6 = 18 damage vs 5.5*8 = 44 damage. (A Chaingunner with a similar setup would have the same accuracy as a pistol user and deal 25 and 20, respectively, with the same setup. And it would use 1 less ammo.)
Rockets deal AoE damage. Give it 4 enemies in blast radius and it can deal 84 damage in a single fire. Dance around cover with reloading and you can kill a large group much easier than any pistol user ever could. Similar tactics work best with the shotgun family, as well.
So, yes, while pistols have the potential to be good, other weapons start off good or don't need as many feats to be as good or better.