It's bad game design to have an optimal strategy that's boring, and then expect players to not do the optimal strategy. Sid Meyers also mentions that "one of the responsibilities of designers is to protect the player from themselves". The optimal strategy should be fun.
That's my point exactly. "I should hold back because deploying my awesome big battleship will eat too many supplies" may be optimal but it's not fun. I worked hard to get that battleship, dammit! Being able to curb stomp some small fry with it is part of the reward for all that effort, but the game discourages it because it's not optimal.
I think deploying your massive battleship to kill 1 frigate loses its fun value very quickly. You can do some 'fun' things once or twice, even if it isn't optimal, but while I smirk when my Paragon absolutely deletes a Kite, the game would not be better if that's all you did -- chew up outmatched opponents.
The problem with autoresolve is that it promotes skipping the 'fun' part of Starsector, the combat. You already have autoresolve for pursuits (which generally does better than actually playing it out, I find...), which prevents the classic autoresolve issue of 'your invincible unit randomly decided to commit suicide in this battle... somehow', or Total War's 'higher difficulty = super imbalanced autoresolve so it's a trap to press the button'. Starsector is still heavily a space combat game. The space combat is IMO the best part about Starsector. It doesn't make too much sense to promote skipping the space combat in Starsector.
Forcing the player to fight battles also promotes fighting fairer battles. Instead of just picking smaller fleets to constantly autoresolve against, it promotes actually finding more challenging battles, since it's a better use of time.
Eh... combat is the main source of fun in Starsector, that's true, but that doesn't mean every battle is fun or worth fighting manually. Starsector tries to get around that with the CR and supply mechanic, by pushing you toward making those fights more challenging for yourself. But that kinda makes it feel like a self-imposed challenge rather than overcoming a real challenge, and a lot of people (myself included, obviously) aren't into that. So they don't do it, take the CR hit, and then complain that CR is annoying. You could say that that's my own fault and that I'm playing the game wrong, and I'd respond that the dev failed in his responsibility to protect me from myself as per Sid Meier's words.
There's this weird incongruity that is difficult to put into words. It's as if the game doesn't know whether it wants to be stat-based or skill-based. Where does player power come from in Starsector, stats or skills? The management aspects of the game point toward stat-based: you scavenge and trade to get cash, you establish colonies, you accrue a large fleet, outfit it with big guns, staff it with officers, etc. When it comes to deployment, the game discourages you from using the power you've accumulated and instead pushes you to fight on equal footing, as if it were skill-based. But when it comes to the actual battle itself, most of your power is in AI ships that you have very little control over compared to more conventional strategy games, so the game has switched to stat-based again. Except you don't have your stats, because you held back in deployment. The game discourages you from using your stats to win (because if you do, you waste CR), and it doesn't allow you to use your skills either (because you can barely control other ships, and your own keels over and dies after a few minutes). The dev doesn't understand what fantasy the game caters to; being able to assemble a large fleet of awesome warships is a power fantasy, but then the game punishes you for using that power and tries to make you struggle and scrape by anyway as if it's some kind of survival game.
The game wants you to accurately estimate what it will take to win a battle. If you want to spend a bit more for a more secure victory, you can do that. To use a RL example, the US does not deploy a carrier group to deal with piracy off the African coast, when a few ships will do the job.
As far as player vs fleet ability, this is where skills, officers, and all the other stuff combines to (hopefully) make interesting choices. Nothing stops you from going with a chain flagship strategy, if it still works, where you deploy 1 ship until it starts running out of CR, then you deploy the next and transfer command, etc. You can also go with the other side of it now, with Derelict Contingent and try to flood the field with crappy ships that have relatively low supply costs to maintain. If you have actually reached the point where you have a big fleet with officers, then you are probably also at the point where an extra 100 supplies per battle is no longer a serious concern, especially now that you can back your fleet up with a strong economic base from colonies. I can't say I'm the biggest fan of how the skills are set up now, but the ideas are there. Combat = you are stronger, Leadership = Officers are stronger (and it seems carriers as well?), Technology = Ships are stronger, Industry = You have more stuff/your campaign layer is stronger.
I think Alex understands his game and setting very well. The Hegemony and Persean League are not first rate powers, having the latest and greatest in technology, with well defined fleet doctrines and strategies. Instead, they are just the biggest fish in the pond, clinging to the scraps of what the Domain left behind. Everyone is just trying to get ships together that work.
As a player, you are trying to assemble your super awesome fleet, but there's significant hurdles in your way, which is the game. It's perfectly achievable, it's rather trivial to set up 3-4 colonies to earn 500k+/month. Once you have that, you basically don't have to care about CR, just take like 2 Atlases and 2 Prometheis full of supplies and fuel, since the credit cost is immaterial at that point. However, the game is IMO best when taking the journey to reach the 'optimal' fleet, not when you actually achieve it.
Project Ironclads was the TC mod that catered more towards the idea of what you mention, and it did a good job of it. But it was different from Starsector, which is why it was best as a TC.