I think a solution that may work is to remove the player rank as the prerequisite for the skills. Instead use the skill themselves as prerequisites in a skill tree fashion.
In this example one has to invest points into the previous skill to move to the next one. Of course the skills would need to be reworked so that they accumulate in conjunction with one another to total a max bonus for end game. Also note, I lumped Assault Cruiser and Star Cruiser into one skill.
Now some skills such as the weapons will need to be set up different than the above as it will be more of a specialization.
So weapon skills will go along the lines of; Starship Weapons – Beam Weapons – Specialty type ( Phaser, Disrupter, etc) or one would choice; Starship Weapons – Cannon Weapons - Specialty type ( Phaser, Disrupter, etc) and the same for Projectile weapons or Mines.
The ships types and weapons as well as ground skills are the easy skill to rework, as it will mostly just be changing the prerequisites. Now for the Starship Engineering and Operation skills, I believe these will need to be reworked completely as of right now they seem to have little to no impact when chosen.
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