In my experience the number of fleets specified in the AI fleet.txt file should be rather low: 10 at maximum but usually 2-5 will be best.
My record was an AI attack with two fleets in a single turn on the same sector. Each fleet had over 500 ships! However the fleets attacked one after the other while a human player would of course make the attack simultaneously. The AI won the combat but had serious losses in the first fleet.
Appearenly the thing is to tell the AI to use only 3 fleets, with 80% ships in the fleets, and to attack only every 10 turns, so the AI can pool its ships.