After playing this for a while here are some of my thoughts:
Helmsman with the 1% flux is awesome
Standoff Tactics is actually useful now
For the Shield skill, I changed the -10% elite skillback to -20% - only getting 10% seemed expensive for a story point
Phase Mastery, changes are pretty good, but I put the elite up to 50% speed, still a nerf, but again, a story point should be very worthwhile
Nearly every skill change in the leadership tree is spot on, excellent job. Also removing all the deployment point limits on the skills is much appreciated
For Auxiliary Support, I recommend upping the supply % for the elite skill. Unless you are playing a very heavy civilian fleet the stock amount isn't much. I set it to 50% and even then I haven't bothered taking it.
Gunnery Implants, I put the elite skill at 15%. With the ECM change I feel like this is fine and again, story point.
Flux Regulation, thank you for removing the limits there 10% is good regardless of fleet size.
Jury Rigging is a very nice to have for exploration and if you happen to have D ships
Field Repairs is excellent as well
A few random notes, I like all the extra elite options, it's nice to have some bonuses to unlock if I have extra story points. Being able to select two skills previously in the same area is very nice as for instance, I like taking System Expertise, but also Missile Spec.