A couple of versions ago, we had a soft-limited fleet size, based on the logistical footprint of the ships in our fleet. This wasn't set up perfectly - there was a basically-mandatory skill to boost the cap, since at default you could just barely field one capital ship - but it did have a number of advantages over the current fixed limit by number of ships.
The big one, though, the one that prompts me to actually write this suggestion: I believe that this change was the underlying driving force for the current game's inflated fleet sizes. When an endgame player can field a dozen Paragons, the sorts of fleets that can pose a challenge to that are, uh, kinda boring and tedious to fight.
I don't like slogging through a pirate expedition multi-fleet blob that's thirty-plus Atlas IIs and supporting chaff. I don't like having to fill my fleet with capital ships to have even a chance at taking on some Tri-Tachyon deserter bounty that's packed full of paragons and astrals and dooms.
And the thing is... as long as the player's fleet is limited by number of ships? Those massive battles have to stay, because otherwise the player will still end up with a fleet full of capitals and cruisers and be able to just steamroll over anything smaller.
So please, bring back fleet cap by logistics. Don't make a skill for it - that was a mistake last time around. Maybe have it scale up by level if you need to? 80 at level one (plenty of room for game start, but you might have to pick and choose carefully if you luck into a salvageable capital ship), up to maybe 300 at max level - enough to accommodate a handful of capital ships, but not enough that you can just give every officer their own Paragon.