[Mars]

I think it's just supposed to do a lot of damage, not variable amounts.

[Prophet]

That doesn't mean that the Prom does variable damage according to target. It means other weapons should do it.
So the Prom can adjust its frequency according to the target to inflict maximum amount of damage. I suppose that damage is limited by the power of the "argon laser". Thus the Prom should inflict the same amount of damage to all targets. This on the other hand means that weapons that do not have dynamic frequency adjustment aparatus cannot change their frequency according to target, thus inflicting different amounts of damage depending on the target hull material.

[IceFire]

Isn't the Prometheus just supposed to detect what wavelenghths will be most destructive to the targets hull material and fire at those frequencies? How can you improve on that?

More power?

As far as I'm concerned this is all just directed energy weapons.  Throw more energy at them and get bigger results.  The Prometheus is just a good design of said weapon and you can refine and make anything better.