One thing that bothers me about the new CR and multiple engagements system is that the side that has the last combat ready ship wins regardless of anything else coupled with the fact that you lose CR after the end of an engagement. So get this, this happened today:
I'd done the exact same thing I always do in Starfarer: Hound into Lasher into Medusa into Onslaught. Only two things different about it this time around: One, I had to add a couple of freighters to help me haul loot, and two, I got there a lot quicker due to the increased value of supplies. You can get a battleship in like twenty minutes, which is just silly. I assume that's going to get tweaked further down the road. Anyway here I am in my almost-solo Onslaught against a pirate supply fleet. And as usual I completely annihilate it. Except this time my battleship was on low CR and couldn't be deployed at all for the second engagement. And the enemy had two or three freighters that they'd held in reserve and hadn't deployed for the first fight. Usually these make a retreat and let me pick through the salvage from the battle but this time they turned around and said: "Oh look, his big scary battleship isn't combat ready, let's stand and fight!" And that was that. My own freighters weren't armed, so I couldn't beat them, and I was forced to turn tail and run.
I mean... what happened there? My battleship was perfectly capable of combat at the end of the last engagement, it was moving about and shooting just fine. What exactly happened to it after the enemy had been defeated that made it utterly incapable of any action? And even if it was incapable of combat, so what? The enemy freighters had like two machine guns each, even if they emptied their entire ammo supply into my ship they would barely have scratched the paint. I could just sit there and wait for them to get bored and go away. And even non-combat ready ships are capable of travel, i.e. movement, so I could have destroyed them by just ramming them. But nope, can't deploy at all...
I found that made very little sense.