I made no such statements that chemical pistol is a overall better weapon than the pistol, only that the w2c is inferior to the by pass nature of the chemical pistol, which you did not address.
Let me adress that.
Mechanical damage with W2C ammo is the all-around most effective damage type in the entire game, no contest. This is because unlike all other damage types in the game, the DR against W2C bullets will never be higher than 35%. That's in theory, in practice it will never be higher than 33% since the highest mechanical DR in the game is 95% (Cuttlesnail). That's without counting damage modifiers from things like Conditioning, but those can apply to other damage types as well, including heat.
All other damage types are ineffective against enemies with high respective resistances or even an immunity. Acid will be harmless against mutants and deep worms, fire will be very ineffective against bladelings or industrial bots and somewhat ineffective against any NPC wearing an antithermic coat, even otherwise irresistible mental damage is useless against robots, etc.
On the other hand there is not a single enemy in the entire game W2C bullets would be ineffective against,
except Godmen of course.
This is the main problem with energy/chemical pistols if you ask me, they get very little support from other sources such as mods, feats or ammo types. If you compare a .44 hammerer and an incendiary pistol without any mods, feats or ammo types, they will be pretty evenly matched. Energy/chemical pistols are solid at their core, they just need more bonus goodies other weapon types get.
Also, if any of the chemical pistols really needs to be buffed, it's the cryoliquid pistol. That thing is just irredeemable crap, I don't think I ever saw a build made around it.