Maybe give incapacitator torpedoes some utility instead of damage?
My idea is that the incapacitator causes an EMP that has a chance to disrupt cloaks (and maybe drain some of the enemy power core, not too much though to make incapacitator spam not too op). This would make it useful as an utility weapon against capitals that are about to cloak (and in general, makes them rethink their energy usage). Because right now, you can only use a bug as a "counter" to cloaked ships.
The EMP could apply to jump drives, too.
Some additional speed & range would be very nice aswell.