Take something significant away from one of them, or from two or them. Something like
- Repair
- Space Yard Components
- Shields
- Resupply Depots
- Plats
- Troops
- Ship Capture
- the ability to target planets
- PDC
- or something
You could also giveo nly one of them each of the following: Fighters, Seekers, Drones.
Whatever you do, the fun part will be making it balanced after you cripple their poor afts.