How to beat the rocket baddies around level 20-30:
Use a repair drone as a decoy (preferably with fully upgraded thrusters). Hotkey it if you have to. Also, arrange your cruisers in a tight circle around the mothership. When you start the wave, quickly look around using the minimap and locate the rocket enemy. Select your repair drone and move it to the rocket. Then, when it targets you, move it out of the way. By then the cruisers should have started shooting and destroying it. Your other cruisers will take out the other enemies. Repeat.