Think of Ships like Navies irl, your fleet can only be so big, before you start having issues in terms of management, and such. One Admiral can only keep tabs on so many things at once. You need to split up the fleet into smaller parts, as realistically this would result in better management for the admiral, making the most effective use of his fleet.
Do not bring out the Realism argument. If you want to know how Realistic Space Warfare would be, play children of a dead earth.
In this game we have FTL, Psionics and working AI. Realism missed this galaxy by a few thousand lightyears.
Forcing doomstacks out:
The thing is as far as managing multiple fleets goes, the AI is so much better it would not even be a fair fight.
There are 3 resources as far as wars go:
Resource (Mineral and Energy)
Navy Cap
Attention
Attention is the one area the AI will actually be better then us humans. Play a few rounds of Planetary Annihilation agaisnt the AI, multiple planets.
One AI can manage a dozen planets as well as one. But you need 1 or more humans to manage one planet at top effectiveness.
The game is
designed so multiple players can command one army, just to offset the fact that the attention demand would be way to high for one player. Without that, it is just a rush to defeat the AI before it can start nuke-spamming you or hit's you with a giant rock/laser.
FYI, if you want to split your Navy into multiple smaler fleets (like ones for bombardment), nothing stops you from doing just that. The maximum Navy Cap that adds to bombardment damage is 200 (for 100 damage on Full Bombardment). A 200 cap fleet of cheap corvettes can bomb the planet down just as well as the 1000 Cap fleet.
Of course there have been a few indications that they might remove armies from the game, wich might change the balance yet again.