Yeah its going to be limited, so what? that's the whole point... if you want to go industry and build ships and trade, your going to have to give up something else to do that, you cant have them all because that would be ***.
As i have said before and a few others, Passive FP/SP per level is a no no, if you want a big fleet that roflstomps everything, you go leadership/tech, you want a very powerful fleet of about 5-6 ships you go Tech/combat and if you want to build stuff you go industry.
And you don't have to re spec, at level 60, you have 3/4 aptitudes completely maxed out with all skills at lvl 10, i know because i dragged my butt all the way there.
About command ships, i think a thread about those were started but never really got anywhere.
If they generated FP, first of all, that means you can have an infinite amount of command ships and a fleet that expands into infinity, wouldn't really work, even if they cost half of the FP they generate, that means that you can have another command ship in that extra 5 FP the other one unlocks, and that would also expand into infinity, if they were to cost more than that, they wouldn't have any good purpose and nobody would buy them,
If they generated SP, yeah.. imagine yourself you have 1 capital ship and 10 command ships, you have all skills in the game and your one capital ship can single handed, destroy the SDF or any other endgame fleet all by itself, (not that it cant do that now) and that's going to need some nerfing, the skills are to powerful.
I have never written this much in one comment, hope it makes sense.