There seems to be a lot of redundant/unused skills in this game, and I hope my suggestions lead to some positive changes, and make skill building more ergonomic.
Firstly, I think a lot of skills can be combined into single skills such graviton generators, particle generators, subspace decompiler being combined into one general skill that buffs science officer abilities, or all power efficiency and warp efficiency skills combined into one. I realize how this might lead situations where everyone chooses the same skills, and to offset this you can make the skills impact different affects to different player officer types, or selection of different bonuses.
An example might be:
Warp Core Efficiency
-higher sector space speed
-higher power to all systems
(combines driver coils, warp core power)
(science) - Higher system power at lower levels (below 50) and higher auxiliary power
(Tactical) - Higher weapons power and some other bonus
(Engineering) - structural integrity/crew alive/other bonuses
This "sub-sections" can also just be made individual skills you invest in, but categorized for clarity and still imparting special bonuses
Particle and Subspace Science (level 0/9)
-Graviton Physics (level 0/3)
-Photon Physics (level 0/3)
-Subspace Computing and Modeling (level 0/3)
You could also make these 'subskills" boost/add affects to officer skills, similar to how placing duty officers on space duty does.
I hope these suggestions help, and I enjoy criticism and feedback.