This is just a minor detail, and it might differ from how the rest of ion weapons work, but... could you modify the Ion Burst series' charging animations so that the shot charges (those bars) fill up one by one? It would look cooler.
Very good mod. Small criticism: the flavor dialogue with my crew members contains grammatical and spelling errors, which kind of breaks immersion for pedants like me.
Pirate Homeworlds: Don't think of them as Homeworlds. Instead, picture them as Pirate Hubs/Heardquarters. Could be from a mafa organization too, or even Cthulhtists (all pirate ships have a Cthulu emblem after all). Why not do an event where you fight an horde of pirates alongside a rebel ship and become friends?
AI-controlled sectors: Not sure about this one. If you want an AI-centered sector, it should be Industrial Sectors, where the only living being interactions should be centered around blue option-based events and pirates.
Re: "It turns out the former slave was a Federation ensign ..." "2) You deserve some rest ensign. We will drop you off at the next possibility." Add comma between "rest" and "ensign." Change "possibility" to "opportunity."
Re: "The mapping computer directs it's drone servant on efficient path ..." Possessive "its", not "it's." Change "path" to plural "paths."
Re: "The station you detect upon arriving at this beacon was apparently targeted by an advanced cyberattack. The crew is dead and the now autonomous operating weapon systems target you." Change "autonomous" to "autonomously."
Most of the times, when you take to piracy your crew doesnt agree and you dont get to fight anyone. Other times, they commit suicide or desert. Only when you have Slug Gel, Mantis Pheromones or Rock Plating, they respond positively at all times. I'd like this added for all race-specific augments. For example:
(Zoltan Crew) You command a vessel of Zoltans who oathed to serve your cause until you've comleted your mission. Their morality isn't affected by any actions you take.
(Crystal Crew) You command a vessel of xenophobic Crystals who see most of the other races as hostile. They're almost thrilled to help you in piracy.
(Engi Crew) Your Engi Crewmembers have pre-programmed moralities, and aren't hesitant nor excited to destroy innocents, as long as it's an order by their captain.
PS: It appears there are no Mantis/Slug/Rock-Crew perks to prevent your crew taking actions agains't you because of slavery. I'd like these added aswell, as Rock culture most likely involves slavery, Slugs are known for their manipulation which may be used for slavery, and Mantis often slave atleast one engi for every mantis ship's crew.
I'm not sure if every alien race should be able to commit piracy and slavery without consequence. If anything the Zoltan should condemn your actions even more often. The Engi one does make sense. I'm pretty sure the crystal wouldn't like slavery and piracy because didn't they leave the Rock because of their violent ways? I thought the Mantis could take slaves without consequence, but if they can't they really should be able to.