Going by "I was noticing that my fleets combat readiness was decreasing to around 30-40% at the highest, while the enemy still had like 60-70%", it sounds like either you were engaging automated ships (which have a longer peak performance time by default) or fleets with ships bigger than yours (which also have a longer peak performance time by default). Safety Operations PPT/CR reduction might not overcome those differences.
Peak Performance Time is time at which ships operate at CR they had in campaign when the combat had been initiated and varies ship by ship, but. Typical values are 3-4 minutes for frigates, 4-7 minutes for destroyers, 7-9 for cruisers and 10-12 for capital ships. After PPT runs out, CR falls at a steady rate of 1% every four second, except for phase ships, which lose 1% every two seconds. Phase ships also lose PPT/CR in their subjective time, and since time flows three times faster in phase space, phase ships tend to run out of PPT/CR faster.
If you're fighting cruisers with frigates, cruisers can just wait for you to run out of CR.
You got the advice to retreat ships when they run out PPT, but unless your playstyle is already heavy on issuing order on the tactical map, you can run out of command points very quickly. There's something of a trick, though, because if you don't close the tactical map after issuing an order, command frequency remains open for a few seconds and you can issue orders for free during that time. If you do that, remember that opening tactical map and unpausing it doesn't automatically switch your flagship to autopilot.
Also another thing is that I should be able to retreat without completely eliminating my enemy while having a large fleet myself.
In the upper right corner of the screen, there's a "clean disengage" indicator. Once it reaches 100% and the indicator switches to a check mark, you can withdraw all your ship and the enemy won't be able to pursue you. If you disengage from a fight like that, though, you won't get loot.
3) It's not really morale but like you said a combination of combat stress to the ship, morale, ammunition, supplies, etc. The moral mechanic you suggest would probably be too confusing/complicated and would like exacerbate the very issues you are having right now.
Not confusing as much as redundant. Combat readiness prevents the weaker side from prolonging the engagement forever and morale would prevent the weaker side from prolonging the engagement forever. The main difference is that CR works on time and morale would work on whatever it would work on.
I did. I didn't put any on my ships as most of them weren't available. So I assume that most of the blueprint type things applied to my fleet immediately. Things that said "a collection of notes that teach so and so skill" or whatever. I was fighting against pirates so they shouldn't have I don't think. Unless they do idk. Also why are pirates so easy? Is it just me or what?
Solar shielding is a logistic hullmod, which means it can only be installed while docked. You can't swap it on the fly, like other hullmods (though you shouldn't, because you lose CR from that).
What you said about CR is days, weeks, months before the actual battle. While of course they can degrade in battle, but they would do so very slowly, and not within the few minutes of battle. Though like what another commentor said, battles seemingly take longer then what they seem, though this isn't put onto the actual calender. Maybe the devs will? I know it would definitely be hard to do. Either way with the advance tech that's available, especially the use of nanotech definitely voids any arguments of the wear of protracted engagements of a few days. Especially when a lot of the ships are many years old and still hold up perfectly fine under good management. You definitely won't lose that just immediately in a few days of combat. You can you store supplies, and metal, and use your nanotech to literally turn it on the spot into something else for combat. I think something should be done to prevent boring ass kiting, but CR is not the way too go.
Present day humans don't have nanobots that will maintain constant engagement level throughout a long and boring battle in a video game. And I don't think there's any mention of nanobots in the lore, only of nano-scale dumb things, like coolants, or accuracy.
That said, I would say there's an issue with PPT, CR and how long battles in the current version last. Mostly that small ships expire way too soon to be of any use against bigger ships and that battles last too long.
I think what he is saying is that when he retreats his ships, there is a period of time where those ships are not participating in combat, but the DP is also not available for reinforcements, so you fleet is effectively weaker. Of course there is not affect on other ships CR when you order a ship to retreat, but the loss of combat power is a problem that has to be solved.
This works in your favour, too, since winning the fight is about breaking the enemy's initial deployment. If you do, then the enemy will not recover his strength. But that's off-topic...
But sure, it's annoying and I'd prefer enemies to retreat after PPT, at least when it's clear that player brought only long PPT cruisers/capitals and waiting for 0 CR would only result in player's victory anyway.
That's another avenue where the player has the advantage, since you can make the effort to deploy optimally and only use much, much more efficient per CR percent PPT-only deployment, while the AI will always burn through CR and retreat ships only after they drop to 20% CR or so, where they can hardly move anymore, anyway.