All the elite skills seem great and very influential except for Systems Expertise. +30 seconds of PPT is very underwhelming compared to all the other elite effects, but the base skill is so good it might need to be that way.
I like the new wormhole entrance sound.
The skills that boost ships with specific foo with a limitation on the amount of foo are interesting, but the limits seem quite restrictive. If you're building a fleet that's going heavily foo, a lot of the time it seems like you'd be better off taking the general skill instead. This is especially noticable with the phase ship skill; trying it out, I find I could decrease the hard flux generated by phase cloaking by 18% at 51 deployment points worth of phase ships (a doom and 2 afflictors) as well as 106 seconds of PPT and a slight bonus to the sensor profile reduction from phase fields, or just have 18% higher capacity and dissipation for all of my ships at 205 deployment points. This seems like a much harder choice than it should be. If I was only using a couple of phase ships or not using phase ships at all, taking the generalist skill would be a no brainer. I've got a significant amount of DP in phase ships, but nowhere near what it could be; if I wanted to deploy 2 Dooms, I'd 100% be better off taking the generalist skill, even though I wouldn't consider that an excessive amount of phase ships. If I was running a fully phase fleet, which is now possible, I'd definetly take the generalist skill over the skill specifically buffing phase ships. These skills seem undertuned in general.
The first two Leadership skills have some issues. Weapon drills is insignificant past earlygame and Auxilary Support would be okay I guess if I ever wanted to use militarized civvy ships in combat; this feels mostly like a wasted skill point. The choice between Wolfpack Tactics and Coordinated Maneuvers is extremely hard if you want to use officered frigates, and extremely pointless if you don't. I want both of these skills, but someone else might want neither. I'd reccomend swapping Crew Training with Coordinated Maneuvers.
The AI handles phase frigates quite acceptably now. I've seen them do things that resemble my own piloting, which is always impressive. However, I've had Afflictors unphase and move too close to friendly Doom mines and instantly die, so there might be something going wrong there. I think they're moving in to finish off a ship at the same time as I'm placing mines to finish off a ship, and ignoring the mines.
Hostile fleets hanging around preventing you from doing things is very annoying. It's especially annoying when you have a mission to rescue someone from a procgen pirate base, and you have to try to engage the fleet outside of the range of the station so you don't blow up the station and the prisoner along with it. Insigificant fleets shouldn't prevent you from doing things like salvaging and raiding, and lone Drams shouldn't be willing to initiate combat just because they've got a station behind them (something that has happened to me).