Potentially long post ahead.
As I've said throughout this thread, from a conceptual level, aptitude points make sense and I support them. They do create meaningful choice and they act as gates to keep the player from outpacing early content. They are also, simultaneously, un-fun and unsatisfying in their current form. From a meta-game perspective, there are few issues I find particularly troubling about aptitude points, less from a technical aspect and more from an ideological one
1.) Officer-piloted ships are almost always more powerful than you.
Because of aptitude points, officers under your command will almost always be more powerful than you. Not only are they able to spend 21 points directly on combat skills, they are not spending aptitude points whatsoever. For the player character to achieve the same result, at minimum they are spending 24 points and at maximum, 30 points. From a pure combat point-of-view, you're spending anywhere between 15-43% more for the same thing. Aptitude points create a massive efficiency disparity between the flagship and officer ships, all other things being equal.
What this means is that I can exploit the system. Pouring points into my flagship means I skip out on many of the fleet-wide bonuses and end up gimping my overall power. So, I turn my flagship into a D-modded junker ship that is totally expendable and transfer command to a Level 20 officer that is piloting the ship I actually want to fly. Instantly, I have a ship that is more powerful in my hands than the AI and has combat perks that are too expensive to get otherwise. I "lose" an additional ship piloted by an officer but it's a fair trade to me. This shouldn't be the case.
Beyond the exploit, there is a bad taste in my mouth regarding officers almost always having more combat perks than me. When I try to balance fleet-wide and player-centered skills, often I wonder if my best ships would be better off in an officer's hands because of my paltry single-ship bonuses. Because the intra-competitiveness of other "god-tier" skills (Loudout Design 3, Fleet Logistics 3, etc.), they almost always "win" over directly increasing my flagship's power. This could be an issue of the Combat Tree not being competitive with fleet-wide Technology or Leadership skills but aptitude plays into it because points I could be spending on direct combat skills are otherwise going to aptitude points. For a game mostly built around combat, something is "off" about my flagship being (on paper) one of the weakest ships I can field. It's not even an intentional handicap: I'm trying to maximize my overall power but because of the inefficiency of aptitude points, it's the player's very ship that tends to suffer! That seems counter-intuitive and incentivizes the exploit above.
As I've mentioned in previous posts, support officers that make fleet-wide skills less player-reliant would go a long way into alleviating this issue. As it is, the player character's skill tree is the only way to unlock these kind of skills currently and that means there is always a "greater good" debate going on within the mind of the player. More often than not, the relative difference in power between a strong flagship, exclusively, and a strong overall fleet is significant so the fleet tends to win. Likewise, if support officers didn't pay the "aptitude tax," they'd likely more efficient than the player character at supporting the fleet (imagine 21 points of aptitude-free support skills)! But this only proves the point: officers are significantly more efficient than the player character at everything they do because they don't require aptitude points.
2.) The Sunk Cost Fallacy
Aptitude points create a sunk-cost fallacy when it comes to picking skills. Because each aptitude point spent could have been spent on a direct skill, there's a certain psychological weight to them that "locks" you into a particular tree. The line of argument goes "I already spent 2 points in Combat Aptitude, I better use it," even if you really wanted to get into Technology for Loudout Design. Not spending points on Level 2/3 perks and placing them into gain-nothing Level 1 Aptitude points becomes a hard sell that perpetuates itself.
Opportunity cost is very real, which is good, but it becomes a bridge too far internally when you've already spent so much to get to Level 3 perks. In essence, the same aptitude points that create meaningful choice also become barriers to branching out once they're chosen. If you're not completely charting your character progression from the beginning, the sunk cost fallacy will tend to steer players toward the path of least resistance (which ends up being singular trees maxed out). Of course, I'm describing a trend toward this kind of behavior, not actual behavior. Aptitude points and their current implementation do feed into the fallacy.
The way of fixing this, also mentioned a lot in this thread, is either making aptitude points inherently better in their own right (via direct bonuses, perks, etc.) so that the mental hill to climb is easier, or to do away with them and work tree progression into picking skills within the tree directly. I.e, all skills are open at the beginning, you need 3 level one skills to unlock level 2, two level 2 skills to unlock level 3, etc. This makes each point immediately impactful while also having longer-term consequences.
Doing the math on that last point, if you were to go straight for a particular Level 3 skill.
Current system:
Level 1 skill : 2 points
Level 2 skill : 4 points
Level 3 skill : 6 points
Result: 1 Level 3 skill. All skill levels unlocked for that tree.
Proposed system:
Level 1 skill : 1 point
Level 2 skill : 4 points (2 Level 1, 1 Level 2)
Level 3 skill : 7 points (2 Level 2, 1 Level 3)
Result: 2 Level 2 skills, 1 level 3 skill, all skill levels unlocked for that tree.
At no point in the proposed system would you ever feel you were "wasting" points. The question becomes whether or not after 7 points a player character is "too strong." In the current system, the same result would require 10 points. If the proposed system were to be put in effect, I'd recommend lowering the initial number of points available from 3 down to 2, as you're losing the necessary aptitude point to pick anything at all.
We also have to take into consideration the number of points available to the player over 40 levels if we lost aptitude. Most players would stand to gain anywhere from 6-9 points, depending on the number of aptitudes they typically max out (I doubt many people max out all the aptitudes, but 12 points is possible). That's an additional 2-3 Level 3 skills or 3-4 level 2 skills. That's a fairly significant increase in player power. You would ultimately be able to get just about whatever you want. Lowering the level cap to 35 would be one solution to create point scarcity and/or removing any bonus points at game start.
Personally, I'd prefer the same number of points but top-tier skills that are mutually exclusive with other trees (i.e. you have to pick one tree at that point). That's the specialization we need to really vary the playstyles. Instead of writing 40 Level 4 skills, just have a few "Peak" skills at the end each tree that can only be unlocked after X number of Level 3 skills are unlocked. They could either be typical Level 1/2/3 progression or one-point wonders. Once you choose one in a tree, though, all the other "Peak" skills in the other trees become inaccessible.