Now, we have uber fleets. The best way to kill a carrier fleet now is with a suicide JU-88. So, how to kill it?
I think the HS-293 (a German radio controlled rocket weapon) would be the PERFECT weapon...its small and fast, so the fleet ack would be nearly useless. How would you defend against it? First, the only plane that should carry it should be the JU-88 (perhaps a better German bomber later). Its pathetic defensive armament will make it easy to destroy before it can launch its payload. Since the 293 was radio controlled from the mothership, it should be automatically destroyed if it is in flight and the mothership is destroyed.
Damage
Best vs. all ships
OK vs. ground structures
Nothing vs. aircraft (to prohibit guided missiles)
Small collateral damage radius
Another countermeasure idea: the best defense against the 293 was using a jammer-something that threw out lots of radio waves to jam the 293 in flight. It will be very difficult to model though.
The only difficult part of creating it will be how it will be controlled from the mothership.