What to choose for first crew skill/perk?

TheKroo: I recommend going with repair skill as your first skill. It does not need to be at 100% to be active. Additionally, at lower levels repair kits tend to be expensive for your wallet, so having a repair skill is beneficial for your savings.
Further more, once you reach the second skill, you may want to reset your skills and use the accumulated experience to take one of the skills that require 100% to be active - such as brothers in arms

You may also want to have a look at this guide.