Well, the enemy of most AoE ships is Starships (one ship with tons of health makes aoe useless). I presume the Orbital Mass driver is still in there though, so i recommend this:
Build a dozen transports and shove in as many bombers and autocannons and anything else you can grab for taking down armored targets. Then, dump them all into the transports and ninja raid that command station. If you're lucky, that will also draw away their wormhole guards. Then, send in your cap of spire and/or Zenith ando/or Flagships, and ahve them shred as much as they can. Then you ought to be able to use your fleet.