The damage buff to Transphasic Torpedos from the Breen set is not very large, and not commiserate with the loss in durability of not having 3-Borg + MACO shields.
Pointedly, while two transphasic high-yield volleys may do a combined more damage than one quantum HY volley, the time between makes it so that the target can quite easily out heal the damage. The best way to think of Transphasics is as a hull-hitting pressure weapon. If the enemy team has a large amount of cross-hull healing available, then your damage should amount to very little. If they are starved for hull heals, you have a reasonable chance of wearing them down, if your team is built around shield-bypassing attacks.
That?s pretty much what I fly with. Breen set, mine beta/alpha with torpedo spread and the universal console that boosts torpedoes and mines by 10%. Add in attack pattern beta to lower target kinetic resistance and you have a pretty deadly setup.
I edited to my chart up above quanum bleedthrough and to-the-hull damage for both. Now, on the face of it you say, "Transphasics do more to the hull through shields, leading to better damage over time." That is true, but consider that is going thorugh the shields. And if it's always going to the shields that means you haven't taken down their shields. So the other person can just be popping hull repairs and negate the effects of the extra penetration. So ideally you should be taking down their shields, and once you do that transphasic bleedthrough doesn't matter, and it ends up being the weakest torpedo. However, if you use quantum then when you take down their shields and pop a quantum to the hull, it makes up for all the lost bleedthrough. And using THY with quantum to the hull creates a staggering amount of damage. So really my point is if you aren't taking down their shields fast transphasics might be a better choice. But then, the other person can just use a hull repair. And if you are getting their shields (which I really hope you are) then quantums are the way to go because they cause wreckage to the exposed hull.
EDIT: Be gald we're debating this like normal people and not rage trolling on each other.
Which actually brings us back to what the OP originally said as in the original post it was made clear that the OP has difficulty stripping shields and timing torps. SO... to sum up... if one is skilled (as you are) at stripping shields and timing torps then Quantum is the way to go... BUT if one is NOT so good at stripping shields quickly or timing their torp launches then Transphasics could be a viable option...
Sounds like the two of you have arrived at a PoTAYto/PoTAHto kinda place
ZOE: "Sir! You paid money for this?... on purpose??"
KIRK: "Excuse me... what does God need with a starship?"
I do not see how. By the time the Quantum?s can fire with shields down Transphasics have already done more than enough damage to outpace Quantums. Normally Transphasics end up killing the target well before Quantum?s.
What I mean is 1 Transphasics salvo on shields and 1 salvo on hull without shields does more damage than a timed Quantum salvo on hull.