As my crew overhaul idea requires too much time and effort to implement, I changed some of my skill ideas into "Superior Crew Training". The modules, called Training Facilities, require only a small amount of space (to accomidate the equipment) and provide minor (but far-reaching) benefits. Crew training modules can only stack 2 per crew type (otherwise you will overwork the crew).

Here are a few training facilities-
Hand-to-Hand Combat: grants bonus to raid and to counter raiding based on tactical officers
Trapsmithing: bonus time added to set traps based on engineers
Medical: decreased chance of crew death based on scientists

And my second research tree is "Advanced Digital Technologies". The modules are called upgrades (with some space taken to put the servers that store the programing), and are limited to 6 (otherwise the ship's computers can't keep up with the data). I also added one of Odragon's ideas on my thread and Redlaw's targeting thread

Here are a few servers-
Comunications Upgrade: decrease to the amount of energy needed to post on someone's comm
Shield Routing: increase shield charge rate
Targeting System: increase the damage cap of attacks against smaller ships
Targeting Scrambler: decrease the damage cap of attacks from larger ships
Cyber Security: decrease the research lost from an opponent's successful hack
Cyber Infiltration: increase the research gained from a successful hack

I like the idea of making skills for crew, as I have said in the two other threads about it. I hope this gets implemented. Good ideas for skills BTW.

As there has been no negative feedback, I will continue to make more:

training facilities-
XTS-9 Chemical Treatment: increased chance of obtaining XTS-9 from XTS-9 Refinement mission based on scientists
Ship Maintenance: decreased upkeep cost based on engineers
Dynamic Evasion: increased defence for every round of combat with the same ship, bonus capped based on helmsmen
Dynamic Combat: increased attack for every round of combat with the same ship, bonus capped based on tactical officers

servers-
Ion Countermeasures: deals 10 damage to opponent when hit with a Containment Missle or Omnicron Net
Pulse Countermeasures: removes 5 energy from opponent when hit with a Positron Clouder or Quantum Flare
Advanced A.I.: +3 to attack, defense, scan, and cloak
Stryll Recognition Seeker: +10% timer duration on rare NPC's