Two things; one, the newer long range missile damage means it doesn't actually do much of anything to any ships unless you have a few dozen missile launchers. They don't 'soften up' the enemy, they hardly even tickle it. However, what might make it a better trade off is to reduce the RoF from 'whenever there's ammo' to one firing every other second, no faster.
Secondly, as a counter to the shield-destroying power of the missiles... have the Zentraedi Shield Generator regenerate its own health over time while powered, but have a higher power draw per shot and power drain over time.