I don't really understand this argument. Past the early game supplies are cheap, you salvage more from fights, and you have oodles of cargo space to carry extra.
Maybe if you take the extra loot skill, but with the severe level cap, I find that unjustifiable.
That is not true. You certainly don't need any loot skills at end game. Early to mid-game, possibly, depending on how well you do in the combat portions of the game.
I've taken all 8 Combat skills and 7 tech skills from start to end, didn't respec nor did any trading, and was able to go from beginning to end without any issues mostly doing bounty hunting and exploration missions in a general direction, and then come back to the core after exhausting the missions in one direction (needed to come back simply to refresh for more missions anyways).
At end game, I'm getting 400 or so supplies from high end bounties (350k-400k). 400 supplies is enough to deploy 6 Paragons. If that's not enough, and you don't want to spend skill points, there are ships like the Shepherd and Salvage gantry which merely cost credits which can improve your salvage - but that does involve doing a trade off analysis of running expenses versus expected extra supplies/fuel along with distance estimates. Which is yet another decision to be made.
So to give a concrete counter example, my end game fleet from my last run with 5 Capitals, 4 cruisers, and 6 cruiser logistics ships carries up to 6680 units of cargo, at 15 supplies per day. Assuming 10 deployments of 240 DP each (Odyssey, Doom, 2 Paragons, Legion XIV say), that's still 4280 supplies left over, for 285 days of exploration time, assuming you don't pick up a single piece of cargo during all that time.
Can you give some in game examples of what you want to do and how you've actually been limited in a real game run? With numbers? Like, after 2 months, I was forced to turn around my fleet of X,Y,Z due to lack of supplies?
While the game does push you towards more efficient play (use minimum resources) it doesn't absolutely demand perfection. There's a wide range of efficiencies which will still improve your game state, just not as fast. Especially later in the game with a fully developed colony or colonies behind you. I mean, there are a number of problems with the game balance wise right now (and Alex admits that), but CR and supplies I feel overall are in a good place, at least in my experience. Get far enough in the game, and you can pretty much do whatever you want inefficiency wise.
Out of curiosity, are you just looking for more and better missions (missions as picked from the start screen, not campaign quests). Maybe an easy to use arbitrary mission generator? A selection of 100 interesting missions, perhaps with some progression? At that point, there's no travel time, there's no supplies, fuel, credits, nor any limitations on what fights what. It's simply whatever two fleets have been picked fighting it out, with no long term consequences. If you want a string of Paragon vs frigate fights, you can do that. If you want an even fleet vs fleet with identical DP, you can do that too. If you want an last stand lone Paragon versus a low tech fleet, that's already in the game.