Look at the DPS versus Burst. Photons have a higher DPS, because they have a shorter cooldown, but the Quantums have a higher burst damage, to balance their longer recharge. Plasma torpedoes have a chance of doing DoT. However, I don't know about any other torpedo choices as I only use Quantum torpedoes.
I'm beginning to think that it doesn't matter. I haven't run numbers, but I"m fairly sure that all the torpedoes of any given level do the same damage over time. The same goes for shields... I'm positive that all the shields in any given tier give the same amount of protection that's just a factor of strength, regen, and protection.
Each has differ damage type, different rate of fire, and different side effect. None are that much better than other, it which works best with your tactics better.
So far, I think the choice of torpedo goes along with your preferred Tactical skill choice. If you just want to use straight torpedoes - go with the photon torpedoes. If you're going to use torpedoes with an attack spread option, go with quantum torpedoes. And if you are going to use torpedoes with a high yield option, go with plasma.
Comments
Photon have higher DPS, Quantum have higher Hits.
As was said before, Photons fire more often vs Quantums that hit harder but cool down slower.
Plasma has lower DPS but has a chance to apply extra damage over time.
Chroniton reduce flight speed and turn rate.
Not sure of the others but you get the idea.
Choose what you want to use.