Honestly piloting and not piloting a ship yourself isnt that big of a difference.
Piloting a good ship can change the battle completely, especially in the end game with max level. Your character has 15 levels and has the most skills of your officers. Additionally, you are not limited to one ship. If you have enough reserves you can pilot a ship to the ground and jump to the next one. This is like 2-3 level 15 officers.
The effectiveness of piloting your ship can vary a lot and depends on skill, fleet composition of your opponent's and your own forces and loadouts.
I'm usually assuming that my flagship alone pulls down more than 300% of its DP in enemy forces. That's easily 120 DP.
The bigger the battles, the less of an impact your flagship will have on it. It will be swarmed more often and while 120 is 30% of 400 it's only 20% of 600.
Additionally, with bigger fleets your logistics become more difficult and expensive. Having a lean fleet throughout the game allows you to save more money and therefore enter the mid and late game faster.
Many of the crisis battles assume that you are very efficient with your fleet and that you can defeat 2-3 fleets at once either with defenses or without (AI inspection).
In summary, don't discount the effect of piloting your flagship. The game works well without it and you can have tons of fun with the strategical aspect of battles, but I believe the balancing assumes you pilot your ship. I believe the divisive opinions on the Persean League crisis are a symptom of this.
Back to the original question: What is a good balance for fleets? I'd start with 500 and increase it by 100 until you feel your hardware gives out or you have less fun than before. Consider other factors like count of officers and supply / fuel costs. I tried bigger battles and reverted it to the original.