Let me lay this out for you:

The extra punch through power to shields of the transphasics seems better on the surface. But when you do the calculations to how much damage you actually get through shields with transphasics (I have done the calculation) it comes out to less than 1000 damage. So if you slap THY on there you get a little more... if a transphasic goes to the hull you lose the potential damage of other torpedoes. Now, quantums. If you are good at the timing you can do far more damage than a transphasic. One quantum to the hull will outweigh transphasic's extra penetration. And then you've also got lots of people running around with MACO shields, which are resilient shield arrays. so the bleedthrough is reduced even more. In the end quantums really are going to be better. You aren't going to be one-shotting cubes in your impenetrable Intrepid class with transphasics like Voyager.