I'm very glad you've brought this up, because there's an important distinction to be made here. In my reading, I've noticed that you (and other board veterans) very often use terms like "reward more" when describing this mechanic—but in practice, what actually occurs is that the player is "punished less," i.e., they lose fewer supplies and less CR at the end of the engagement.
This may seem like splitting hairs or semantics, but it really isn't. In psychology, there's a distinction between positive reinforcement and negative reinforcement. Taking away more of a player's supplies and CR because they didn't finish an engagement as quickly as they could have isn't a "lessened reward," but is in fact an "increased punishment" and a textbook case of negative reinforcement. This works both ways: A player who finishes an engagement quickly is in fact working to minimize his punishment, not to maximize his reward. I know that "punishment" has certain negative connotations, but I'm (trying to) use it very neutrally here.
Psychology aside, this has practical implications as well, and it ties into my point about AI fleets being throwaway. During extended voyages, the player's goal is usually to lose as few supplies and as little CR as possible from one week to the next until next reaching a safe port. This makes sense, but as I've mentioned, the AI aren't playing by the same rules. Given all of the relevant factors, I believe that CR loss weighs a little too heavily against the player as currently implemented.
So that's a very good point, and I definitely agree with you as far as the principle goes. It's also something I've been trying to be more aware of as a general design point.
But! I think there are actually two different things we're talking about here, as far as "reward" and "punishment". There's often not much direct reward from fighting, since - well, it *can* be profitable, but oftentimes you're fighting to get to something else profitable, such as salvage from a derelict, a bounty, or a trade fleet's cargo - so any sort of direct reward, there's just not much potential for.
So, basically, you can make the decision to spend less, if you're confident in your skill and your assessment of the engagement's difficulty. That's not quite a "reward", but it also doesn't feel quite like "lessened punishment", at least, not to the same degree that running out of CR in combat does. Where you do get into solid reward territory is when you're able to collect on more of the indirect consequences of fighting - such as bounties and salvage - more effectively, because you're making better use of the ships you've got. Whether it's because you're able to keep the overall CR higher, take on tougher enemies with a smaller force, or simply stay out on the fringes longer, you get to more *non-combat* rewards by doing better at combat.
Going back to in-combat, once you're out of peak time and CR starts ticking down, then I think we do get to the point of "lessened punishment", feel-wise. But that's already a "you were either desperate and didn't have more ships to use or you made a mistake and should have used more ships" state. So, yeah, you're avoiding punishment, but things have already gone wrong for you at that point, if that makes sense. It's not something you ever want to aim for, right? It's cheaper to deploy 3-4 frigates than to deploy one and have it tick down to 0. If you get to that point, you really *are* trying to cut your losses after things going bad. So if it feels like that, then that seems rather appropriate.
It's not going to the other extreme of "more is always better". Rather, it's moving away from the extreme of "one ship is always better" towards the middle, and putting a greater emphasis on player skill in determining exactly how much is optimal.
I don't necessarily disagree with you that there ought to be a balance or happy medium. In Escape Velocity Nova, for example, which I'm sure you're aware of and have probably played, a single Pirate Valkyrie Class IV with the right outfits could take on an entire small fleet of Federation carriers by kiting. Although fun in a storytelling RPG where story came first, I agree that it's a bit much for a crunchier game like Starsector.
(Am aware, of course, but haven't actually played it. Or may have played a demo at some point? Either way, not familiar enough to comment one way or another.)
Excellent work on this game, by the way. It looks beautiful and plays smoothly, and seems to have a lot more complexity under the hood compared to when I first played it and it was basically just a fleet vs. fleet brawl-a-thon.
Thank you! I'm glad you've been enjoying it.