Targeting Analysis: it's a bit weird the bonus is just to capital ships now.
Impact Mitigation: it now protects from small strength hits more than bigger hits, which I'm not sure is a good idea.
Standoff Tactics: it's better than Ranged Spec, since it works for more than two ships in the game.
Phase Mastery, Phase Corps: I suspect they will still be problematic.
Systems Expertise: it's a real shame you nerfed it, because it was pretty fun for most ships that aren't Doom.
Missile Specialisation: it stacks with ECCM, missiles are so fast now.
Officer Training: spend story points to spend story points... Come on.
Energy Weapon Mastery: what's up with that EMP resistance? It's not much, but it's weird it's there.
Special Modifications: again, spend story points to spend story points.
Automated Ships: it's hilariously OP now. Getting a Radiant for a single skill point is incredible value.
Colony skills: they presumably are the best moneymaker skills, making other (mostly industry) skills obsolete. It's in a similar position as Automated Ships, in that it isn't immediately strong, only after you can get what makes it strong, but then it blows other skills out of the water.
I also have more fundamental issues with what you're doing with those skills, but you have heard about them already.
Tis a mod, and a customisable one at that, the base game skill tree is hilariously out of balance as it is, why the intense scrutiny for this?
Big fan of this OP, will let you know if any issues come up!