If you want to deal with Doomstacks there is a very simple and more fitting way. Fleets without an Admiral get negatives to fighting due to co-ordination of ships becoming harder the larger the fleet becomes, make these negatives grow the larger the fleet becomes. Give Admirals an attribute that allows them to counter act this negative based on their level. So a high level admiral can have more ships under his command before the negative kicks in. Then the devs only have to worry about a few numbers for balancing. At what size of fleet does the negative begin, at what rate does the negative grow per ship or number of ships added, and what amount of negative does the Admiral reduce it by level. Expose this to the modding community and people can also do balance mods of their own.
It's also more realistic, as logistics and co-ordination would be the biggest downfall of large fleets, and simpler to balance for whatever size of fleets the devs want to see.
As for clumping fleets together due to the restriction, Admirals already cost influence, and there are limits to how many total leaders you can have anyways so that is not that much of a risk.
Edit because me no speel well
It's also more realistic, as logistics and co-ordination would be the biggest downfall of large fleets, and simpler to balance for whatever size of fleets the devs want to see.
As for clumping fleets together due to the restriction, Admirals already cost influence, and there are limits to how many total leaders you can have anyways so that is not that much of a risk.
Edit because me no speel well