Hm... I think I'd prefer to keep the current system, and just... add something to it, to make it more than "just" a weapon. So... phase missiles. What might be a reasonable side effect of firing such a device?
Maybe firing shifts the ship slightly out of phase for a moment, granting a temporary 10% damage reduction?
Maybe firing it temporarily disrupts the phase drivers, increasing the cost to activate phase cloak (or outright disabling the phase cloak)?
Maybe the missiles send telemetry data back to the mothership, temporarily boosting weapon range as if they were sensor drones?
All of these, of course, would need custom AI - but with lazylib's range-finding methods, that shouldn't be impossible to put together...