You could try reducing transports’ defense value. If a transport rolls a 1, roll again and only hit on a 3 or less. This would effectively halve their defensive capability.
You could also try using the transport rules from the new Anniversary game (see pages 13-16, 18-19, 21 and 31). This is a bit more radical approach, and may require tweaking the setup a bit to counter the reduction in combat strength of some fleets.