When Alex originally brought up "Meaningful Choice" in regards to the skill system, I was all for it. But looking back, I've realized that terminology is vague and honestly kind of useless. What makes a skill "meaningful" (ie, has a significant impact on the experience) or a "choice", isn't really up for debate, but sets such a low bar that it doesn't really have significance in of itself. Sure, limiting the number of points a player can have makes each one more significant, but so would making each level a struggle to reach, or making each skill exclusive from a set.
Skyrim has a system where you can be great at everything, and yet perks/skills are still significant there. You can only level a skill you are using, so you can't level two-handed and one-handed at the same time. Each takes investment, though you can switch at any time and level them both it takes twice as long and a concerted effort on you part. Plus, attempting to level literally everything at once would weaken you to the point that the game becomes impossible (as long as you're playing on higher difficulties at least). So you still have to focus on a core set of skills at least until you hit really high levels.
Saying that the current system is better because each of the choices is more "meaningful" is true only if we assume that the skill system's quality is solely judged based on a very technical and rather arbitrary definition of the word "meaningful". By this definition, why not make it so you only get one skill point, accessible exclusively by killing some ungodly powerful boss? That would make the skill system even more meaningful, and by that definition, categorically better.
In the end, it really doesn't matter if the new system is technically more "meaningful" if it just isn't as fun and that's subjective. While the new system is marginally more fun to some people that specifically like to test the confines of the system itself, it's significantly less fun to people who just want to play the damn game and have a sense of progression.
That's ultimately where I feel the new system fails by the way, in the sense of progression. Really, Starsector has this problem in general. The usual fantasy of an RPG is to start out small, then work your way up until you can kill god or something. While the skill-curve and early-to-mid game in Starsector do that fine, it drops off hard in the end game. At some point, you're facing fleets that no matter what you do will always be stronger than you. The [REDACTED] will always have better ships than you in terms of sheer stats and officer quantity. The only advantage you can have over them is by min-maxing your builds (your skills, officer skills, and ship fits) and just sheer player skill. That's it. And once you reach that point, you have to play as hard as you can every time unless you use some kind of exploit. You literally hit a progression wall, where no progress you make will ever be "Meaningful" again. Oh sure you can overcome the challenge, for whatever that's worth, but there's not a meaningful reward behind it, just... more of the same. It's why the most popular mods focus on endgame activities, and people are feeling the lack of HVBs and IVBs really, really hard right now.
All in all, perhaps I went off-topic a bit, but this is more of a "yes and" to the OP than anything else. I completely agree that the game is constricting player choice as it continues to funnel the player into more and more combat, and I agree that's a bad thing since the game refuses to actually reward you for it to any degree of significance. I also agree the new skill system is a part of that problem, thought I also argue it's a result of... well there's just no way I can put this nicely, but what I think is simply poor design choice. Sorry Alex. I love you, and I appreciate all the work you put into this game, but I also think that your decision for the direction of this game is wrong. Of course, I'm not a developer, this is not MY game, and I don't have any right to tell you what you should or should not do, but I also feel that I would regret it if I didn't express my opinion.