So I've been playing this new update a lot and I've noticed something a bit weird. I'm not sure if this was the same in previous versions or not, but it seems the enemy deploys his ships based on the ships that you yourself deploy, which can change the difficulty of a battle in really strange and counter-intuitive ways.
This is what happened: I had two destroyers against a pirate force of several frigates, destroyers, and a cruiser. I kept reloading the game over and over trying to defeat this superior force, but no matter what I did I never managed to defeat the pirates without losing the AI-controlled destroyer. There were just too many enemies, despite my best efforts they always managed to overwhelm and disable the other destroyer. Finally I grew frustrated and thought to myself, screw you, stupid AI Hammerhead, you're just a liability, I'll do this on my own! And so I went in alone and to my utter surprise and bewilderment managed to handily defeat the entire enemy force right away.
I went back again to figure out what had happened and it turns out that I was getting beaten because the pirates were deploying their entire force against my two destroyers, which enabled them to easily overwhelm me. But when I only deployed one, they sent out only a smaller force that I was able to easily kill with my high-level character and very powerful flagship. The first wave of enemies was dead before the reinforcements made it to the fight, and the first wave of reinforcements was dead before the second one arrived, etc. Where the entire enemy force was able to easily overwhelm and kill my two ships, when I only deployed one I was able to defeat them piecemeal.
The point is this: I was at a disadvantage, outnumbered and outgunned. I find it very strange that putting myself at even more of a disadvantage by only deploying half of my force made the battle easier.