Personally I'd go for the Pulse Launcher and Harpoon on [i]Dragon[/i] as its main weapons, and then have the torpedoes and sonar as the special equipment.

It's be nice to have the option to switch out the torpedoes for the Gatling Chest if we dealing with a land-based Kaiju attack, but only if the Shatterdome received sufficient warning for the work crews to be able to handle the refit fast enough.