I'm aware that at the moment transphasic weapons aren't really pulling their weight and the devs have acknowledged that they need a little love. This is a suggestion as to how they could work in the future.
Instead of having an improved shield penetration, they could be changed to improve their actual ability at damaging shields. Not so much that they can be used to force a ship to drop their shields, bt enough so that more damage "overflows" into hull damage.
I will demonstrate below:
(note, I will be fudging the numbers here to make it easier to demonstrate, but hopefully you will get the point)
Quantum torp vs transphasic
Vs a ship with 0 shields
Quantum = 1000 damage
Transphasic = 800 damage
Vs a ship with 200 shields left:
Quantum hits, doing one quarter of damage to shields.
Shield damage 200 (800), 200 damage overflows to hull.
Transphasic hits, doing one half of damage to shields.
Shield damage 200 (400), 400 damage overflows to hull.
This would mean that in scenarios where the enemy shield regens a tick just before your attack hits (particularly useful for mines) you would achieve better damage than with a weapon with a higher base damage. They wouldn't be overpowered, as in situations where you can guarantee 0 shield you will achieve better damage with another weapon type, but they would still have their use.