I remember I once wrote, before 0.95 was released, that I won't mind changing how skills work, if tier 5 skills will become suitably powerful. I am still calmly exploring it, but many are of the opinion that new skills are worse. Perhaps that tier 5 skills aren't suitably strong is a part of the issue.
In 0.9.1, Fleet Logistics was a strong skill, because you got guaranteed recovery of officered ships, -25% ship maintenance, +15% max CR, +30% accessibility for colonies and +25% fleet size for colonies. This skill was strong, because it gave you various bonuses that were generally useful. All this for 3 points for aptitude and 3 points for the skill, or 12% to 6% (less if you pick other leadership skills, since it means aptitude cost becomes a smaller part of points spent on leadership).
In 0.9.5, it was broken into several parts. L3L/Crew Training became the part that increased max CR, and it costs 20% of your points to get there. L5L/Space Operations became the colony boosting part, it costs 33% of your skill points to get there. The supply part became Makeshift Equipment, kinda. Cost is 20% of your points. Guaranteed officer ship recovery is gone. To get all these benefits, you'd have to spend 53% of your skill points.
Even if we ignore Makeshift Equipment, you have to spend 33% of your skillpoints for what once costed 6%-12%. And Fleet Logistics wasn't even the skill that was considered the most universal, the safest pick.
Because that was Loadout Design. What became of it? It's Special Modifications now, which lets you integrate one additional hullmod, and gives all ships +10 max caps and vents. Many people consider it the best skill, but since I'm a bit story point anxious, all it does is let me put some more caps on Omens and some more vents on my Paragon. Other than that, I think I have integrated more than one hullmod on a ship only once. Special Modifications isn't very good, since it only benefits capitals and some specific smaller ships. Caps and ships like Doom or officer ships are where you would put your 3 s-mods and with the most extra OP, they are most likely to benefit from additional vents. It's no longer a skill that buffs your entire fleet, but one that buffs your elite ships.
What it does differently from Space Operations is that it comes at the end of a generally good tree, so it doesn't feel like a wasted point.
I think that a part of the issue with new skills is that tier fives just aren't worth 33% of all of your skill points and the only reason people get them is incidentally, by investing previously 4 skills into the tree and deciding that tier 5 skill they're getting is worth 1 skill point they spend now, regardless of past choices.
I don't really have a big issue with skills as of right now, I'm mostly thinking out loud. Except for the combat tree, where it's actually worse for your flagship performance to try and double-dip combat tree, with the better option being spending points in all other trees (L1L for damage, maybe L3L for CR, tech 2, 4 and 5 for obvious reasons, I2L or R (I've got a preference for R, though)), which may or may not be a failure in design.