The abilities are categorized into 5 levels and you can't select an ability in a level until you have one ability in the previous level (excepting level 1 obviously). The abilities cost a number of skill points per their level (i.e. level 1 abilities cost 1 point, level 2 cost 2 pts, etc) and your captains earn points via experience gained in battles and each subsequent point requires more experience than the last.
What this all means is that its an ever increasing requirement of experience to get the next point, and skills in higher levels need so many points to open up skills in lower levels in order to make them even available. In other words, even in Closed Beta with its increased rewards to speed progression I never got and level 5 skills.
There are two extreme approaches you could take to gaining skills. The first approach is breadth first where you use your incoming skills to get all the level 1 skills, then all level 2 skills, etc. The second approach is depth first where you get one level 1 skill, then one level 2 skill, then one level 3 skill, etc. The advantage of the former is that you get lots of skills more quickly, but it means it will take you even longer to get to the higher level skills since each skill point takes more and more battles to earn. Another issue is that not all skills are very useful or even apply to every ship class, or even every ship in the class line. For example, while early USN cruisers have torpedo tubes later ones starting at tier VI do not so taking skills that work on torpedo loading would be wasted.
Oh, I should mention that you can move captains from ship to ship and retrain them to the new ship either instantly using Doubloons (i.e. gold) or after getting so many experience points (the number depending on the number of skills he currently has) during which the skills' effectiveness are 50%. This allows your captain to develop and grow with more skill abilities as he progressed up the tech tree with you.
I tried both depth first and breadth first training in the Closed Beta while I was learning things and decided that I would concentrate on depth first to get the best skills and back fill later on.
(If you make major mistakes you can pay gold to re-allocate all the skill points, the more points to re-allocate the more gold it takes).
Whew! Got all that?
As I am working up four lines (IJN Battleships, Carriers, and Destroyers along with USN Cruisers) I have been working on the same four captains. The cruiser and battleship captains were with me at the start while I picked up new captains for the carrier and destroyer when they became unlocked. I'm going to go over the skills I've picked for my four captains and the reasons.
The level one skill is to get the most out of my secondary batteries for fending off destroyers, torpedo bombers, and getting extra damage on enemy cruisers and battleships.
Second level skill I went with faster turret rotation, even though its only 0.7 degrees/sec more for the big guns, every bit helps with those suckers and makes it more possible to be 1/2 turning and still track.
I had some debates on level 3, but went with the extra repair for more hit points back in a pitched battle.
And since my captain is close to have four points to spend, I've already picked my level four skill out:
This will work nicely with my level 1 skill to further power up my secondary batteries and AA defenses.
I just recently got my Omaha tier V cruiser, so the captain is still retraining.
Again, no other skill but improving the secondaries and AA guns appealed for the cruiser, and...
... Same with level 2. The turrets track really fast on the Phoenix and Omaha with this skill and make for excellent Destroyer hunting.
Overall, not happy and *might* respec this captain later.
My Destroyer captain only has 2 skills, getting close for his third though.
I find this extremely helpful for telling me when to start turning and looking for cover or getting out of range. Destroyers are dead if targeted too long.
For a ship designed around delivered torpedoes, this skill comes in very handy.
My tier V Zuiho carrier has some very different requirements!
First off he uses the Expert Rear Gunner to give torpedo and dive bombers some extra defense against fighters. I've killed a few over time and it helps keep them alive longer.
Again, torpedoes are key for carriers so reloading faster seems like the best option.
I agonized over the level 3 choice because I'm in a IJN carrier and they tend to be seen mostly without fighters and concentrate on damage and avoiding enemy planes, but there was not another skill in the level that appealed.
So there you have it! My current captains.