Re: Skills: I think its important to remember that respeccing uses an infinite and (so far for me at least) plentiful resource in story points. If its worth spending a story point (or 2) on hullmods for a given ship, its worth spending a respec point to select the correct skills for it. This is particularly applicable for combat skills, but it applies for things like colony skills as well if the player finds that they would give a big boost when they reach that stage of the game. 15 skills may be restrictive, but its supposed to be, and we can change up our builds at a moment's notice.
The permanent skills locking in those trees is not great and contradicts what I was saying above: I would vote for a more elegant solution that gives full respeccing.
Looking at the combat tree/skills in particular, there are some extremely powerful options in there. I would happily loop around for both the second and 3rd branches for a combat focused character (not saying this is optimal, just that I can see doing it). The first one being a dead skill (fighters) hurts quite a bit, but its worth it IMO for being able to stack those 2cd and 3rd branches. I'm surprised and a little skeptical at folks calling the level 5's bad: the missile skill is massive for any ship that's using missiles extensively, especially with Elite (I haven't tested it yet: I need to see if the ROF increase applies to just when firing missile bursts, or also to missile cooldowns, but I'm guessing both). The system skill is crazy good too on the right ship: imagine a Doom with an extra mine, that produces mines 50% faster, and can launch them 50% further (probably the most extreme example).
For the Elite skills: Story points are a cheap resource, much cheaper than skills, but one that doesn't want to be wasted, so these are almost automatic buys on any skill that you don't think you will retrain. Since I don't fly carriers (or at least won't this playthrough), the navigation elite is an autopick that makes the 0 flux boost into the 0 generation boost. It is a bit annoying that these points are completely lost if the player respecs out of them: I would want a special case where if you just swapped the skill for its counterpart, rather than losing the skill level entirely, it was kept. This is particularly impactful for technology 2, because both those elite skills are insanely good, but depending on ballistic or energy based ships.