If it takes 12 dead levels to get all the "optimal" skills then I have serious doubts about your build being optimal anymore. This suggestion would always allow the player to get some fleet skills and some flagship skills even if they focus on one aptitude, which seems ahead of the current system to me.
Maybe, maybe not. It just means QoL gets shoved in favor of combat boosts, personal or fleetwide. I never take Navigation despite wanting it badly due to lack of points.
For example, currently, carrier specialists need max skills in three aptitudes. Leadership 3 is a given, but if you want to be the best carrier pilot, you need Combat 3 for Helmsmanship 3 alone due to how game-changing it is for carrier flagships (engaged fighters put flux on carrier like shields do, which kills the zero-flux boost... unless you have that perk). Also, player needs Loadout Design 3 for more OP since carriers are extremely hungry, and great for all.
For everybody, Loadout Design 3 is great for everyone. In Leadership, Fleet Logistics 3 is great for everyone (less maintenance cost, more CR to outlast cowardly AI), and Fighter Doctrine 3 is great for any fleet with carriers (which I suspect is the vast majority). That is six for aptitudes. For Combat, there is some perks at 3 that are great for a variety of builds if not necessarily universal for all builds. Helmsmanship 3 is non-negotiable on carriers because it is such a game-changer. Finally, Industry. If you want to play the exploration game, you need max Surveying and/or Salvaging. Industry has some gems, but it is the most expendable aptitude. I completely eschew Industry despite relying mostly on clunkers.
Perhaps the suggestion might help... or maybe make it worse by scattering must-have among all four aptitudes instead of the current distribution of must-haves for everybody in two aptitudes and more for various character builds.