Aha! Okay; I got it, thanks In fact I had taken quite the same approach; I wanted top of the line systems, and thus took pulse phasers and quantum torps without looking a lot through the rest. Seems like I was right, for the firepower is the maximum I could afford with the base rules.
But maybe two torps launchers were too much. Hell, even the Defiant only has one. I'm thinking of switching a torp launcher for another pulse phaser array - the ship has taken quite a beating in our last ep, and will need some time refitting at DS9 - rearranging tactical systems on the prototype could be the decided schedule. That would up the penetration from 4/4/4 to 5/5/4 while lowering torps from 5 to 4.
Hmmm... That may be the way.