Passive skills can be unlocked via Medals.
Advanced Colonization System is essential for fast capturing ships, and a decent idea for every ship since you can be pressed into capture duty at any time. Ground breaking technology is pretty powerful as well, and can potentially allow you to out-upgrade your opponents. Scientific officer is usually a good idea, since the chance of needing to purchase faction upgrades is very high, even if its just Advanced Colonization or Experimental Armageddon. If you're willing to forgo one of these skills, you can pick up Fleet Customization if you find yourself using a lot of escorts. Short Range Scanner generally isn't worth it.
Advanced Emergency Pod is a given. Death is a near certainty, so diminishing the downtime is wise. High Ranking Officer essentially gets you an additional 25% CP, at least on the per-second level, so should be chosen soon after. After that, it's just a matter of what you're doing. In general, it will come down to High Energy Turn (better for slow ships), and Evasive Maneuvers (best for speed reliant ships). Priority Officer isn't used as much, since going home due to damage usually means the portal will be camped by a team anyway.
Makeshift Repairs reduces the chance of the often fatal engine damage, making it a top choice. After that, Veteran Engineers allow you to shoe-horn in extra upgrades when you only have enough CP for a lower number of them, as well as save you CP over time. Your third upgrade will depend on your ship: shield ships should take the Derivation Device, Armor/Hull ships should take Automatic Repairs, and fast ships should occasionally take Asteroid Ram on maps where they can backdoor by driving through asteroid debris fields (not big asteroids!).
|Legendary Marksmanship||The scatter angle of projectiles fired by the ship is reduced by 50%. Improves the closing speed of the Artillery ship's dispersion template.|
|Quick Targeting||The turret's rotation speed is increased by 5 degrees per second.|
|Mining charges||100% more damage against asteroids.|
|Veteran Gunners||The cost of weapon upgrades is reduced by 10%.|
|Ballistic Tracking||A stealth enemy ship struck by projectiles fired by the ship's weapon systems is revealed for a period of a few seconds.|
Much less important passive skills reside here. Veteran Gunners is important though, as it serves the same role as Veteran Engineers. Sluggish ships will probably also want to pick up Quick Targeting for better turret rotation speed (that combines with the better ship turning speed). Legendary Marksmanship is also essential for long range ships, especially the Artillery. Other than that, it doesn't matter too much. Asteroid charges sort of helps with backdooring, and ballistic tracking can occasionally knock a cloaker out of cloak.