I am an outlier of this game...
I don't like combat very much, I mean, the combat in this game is brilliant and one of the reasons I come back to it, but what made me buy the game way back into 0.6 something was the fact the market had just got introduced in the game, and I am a sucker for trading games.
The 4x elements (specially if you have "exerelin") just made it better.
So that is the thing, for me this is a sort of "first person" 4x + trading game, I don't care much for the (fun) combat.
Still this let me realize the problem with the new skill system is exactly this: it was made with only one playstyle in mind, and destroyed all others.
For example, why colony skills require you to reach level 20 and not get any combat or tech skill? Because colonies right now are the reliable way to build megafleets of the ships you actually want, so to prevent combat-focused players from mowing down the entire game with super ships, colony-boosting skills for that kind of nerf.
Same applies to some other playstyles (for example players that just love smuggling... what is the issue with smuggling? it is that they can rack up ridiculous amounts of wealth quickly and go around buying the best ships right off the bat).
Fixing the balance of the game would be one thing but... this is not what this thread is about, this thread is about the new skill system.
If the next iteration keeps the tiers and choices, what it should do is plan things in a way that certain players can always get all skills they want without feeling penalized, for example it should be possible to get 4 colony skills with some spare points for other stuff, it should be possible to be a super smuggler and have a few spare points, it should be possible to make your entire build around having a fleet of carriers + fighters, etc...
One of the most easy ways to do this is split each aptitude into two "playstyles" when desining, for example industry can have half of the skill slots (one for each tier) dedicated to "industrialist" players like I am, and the other half to "smuggler" players.
Tech you can easily split one half into QoL skills to buff exploration and whatnot, and the other half to buff more combat-oriented buffs (like phase ships, shields, energy weapons), this way people won't even complain about having to respec if they change ship, if the guy IS a combat-nut player he knows he can safely pick 1 skill of each tech tier and be always prepared for any ship, with the downside he won't have the exploration buffs for example (assuming he also spent the rest of his points in combat and/or leadership aptitudes).
Another way to do this is what people suggested previously, and resemble a bit the old system: have the "square" with the aptitude icons, have a number that shows how much points you spent on them already, and unlock tiers based on how much that number rises, so you can make something like require 5 points for tier 5 skill first time, 8 points for tier 5 skill second time.