I often find when I'm exploring that I leave most of my big hitters at home, unless I'm specifically farming a red danger system. Do you find that you need the capital size haulers/fuel ships for exploring Megas? I've sometimes run out of cargo space for low value stuff after a good vast ruins haul, but most of the time I've never felt the need for Atlas' or Prometheus' other than leaving behind metals.
In my last game, I started most exploration late in the game. Early game, I raided worlds for blueprints and money (three of the industry worlds have poor defenses), and chased zombie pirates (base bounties).
For general exploration, I use a war fleet with some explorers because I expect to fight high-powered enemies (relative to my fleet) along the way. And I want burn 20, so Augmented Engines on the biggest class of ships I have. If I chase bounties or Ordos, I want to explore planets nearby too.
I need capital haulers when I bring multiple capitals to match the enemy. I may use Colossus, but once I start getting lots of junk from combat, I swap for Atlas. Also, I would like to explore the whole sector, but I explore maybe third or half at most when I obtain my final endgame fleet. However, endgame is my favorite part of the game, so I play with a big endgame fleet for a significant amount of time.
Colossus is okay. I use those until I need other things more (like lots of Afflictors or more Drovers). Tankers have no such counterpart, so it is Prometheus once I bring the battleships.
My sub-capital civilians in my late game fleet are one or two Colossus III (raider ship with some capacity) and one or two Shepherds. And two tugs - more than that eats too many fleet slots.
That said, I don't understand using Moras to fill out an exploration fleet.
Mora is still a dedicated combat carrier, even if it has exploration mods. It can carry bombers to blast an annoying battlestation (if I do not have the ships to cheese those fights) or it can carry fighters to seek-and-destroy the annoying cowardly AI enemy ships. What am I going to do if I remove an exploration mod from the Mora, upgrade the missiles from a cheap Hammer Rack to Typhoon Reaper pod, or add some other luxury?