The problems at the (later) stage of the game when most battles are pursuit are thus:
* Deploying bigger ships to take out weakened and/or non-combat ready ships is an unnecessary drain on supplies and CR, unless it has a flight deck (e.g., Atlas, Odyssey) and you use fighters.
* Bigger ships often cannot catch up to the smaller ships that are fleeing, those enemy ships most likely to survive a previous melee.
Frigate swarms, when powerful enough collectively to kill everything, including defense/security fleets, within two or three minutes, while taking minimal casualties at worst, are useful for fighting everything. Bigger combat ships are useful only for fighting ever-decreasing number of larger battles and/or flight decks.
In previous versions, frigate swarms were viable, but were very hard to kill defense fleets without taking casualties (unlike cruiser or battleship spam), and they could not take as much loot as a fleet of bigger multipurpose ships. In 0.6a, enemy defense fleets without a Paragon in them are easier than before, and all frigates need to do is kill enough to "defeat the fleet" and hit [Esc] if the survivors are ready to finish off one of your wounded frigates or the stamina clock times out. Then the swarm can mop up survivors in the follow-up pursuit battle, when some of those deadly bigger ships become non-combat ready and sitting ducks. As for loot, with so much from salvage, only freighters can have enough space for it all.