This new system does not achieve it's goals of diverse gameplay, meaningful choices. Full stop. How do I know this ? Because there are ~3 skills that really change gameplay... AI ships, SMods and phase skill. And really given the hullmod options for SMods being mostly stat buffs, I could argue it's only 2 of them. This is a frustratingly false dichotomy that a very restrictive, sparse system by definition makes the skills more meaningful/impactful. It actually matters what the skills do. At least half of the current skills could be copy pasted into the old system!
If you want diverse gameplay and meaningful choices these capstone, end-tier skills need to significantly open up and/or restrict fleet comps and play styles. The other design option, in the constraints of this system, would be synergistic vertical themes. For example, the entire L/R line of a tree would gradually buff a single playstyle or fleet comp, such as carriers, phase, etc. Essentially a class system.
Remove the 4 separate trees, balance the skills across horizontal tiers, and offer game changing end-tier skills at T5. This would alleviate much of the negative feedback about wasted picks, restrictions, etc.
Like Locklave I too stopped playing after 1 playthrough, not just because of the skill system, but the opportunity cost that it took to implement.
Finally if the goals are as stated, why a skill system at all? Why not have players only get these sort of game changing abilities through in game accomplishments? Hunt 100 radiants, do some story point quests with some bar contacts, explore some hidden location and BAM! you now have AI ships....