I think the commander skills are actually a great improvement for cruisers, less so for BBs and DDs (though some BBs like Yamato profit, others like GK and Montana do not). But priority target is such a useful skill on cruisers. HEAP murders BBs, especially if you spec for DE as well. Don't be a potato and take it on anything that does not have 150-155mm caliber.
Here are my captain skills so far for my ships:
1.
US BBs (except Missouri)
Tier 1. Preventive maintenance allows you to switch Main Armaments Mod 1 for Aux. Armaments Mod 1, which makes your AA surive far longer. Double Catapult fighter is great to fuck CVs
Tier 2: EM for extra turret turning
Tier 3: SI for extra heal
Tier 4: CE for stealth, AFT and MAA for ruining the day of any CV.
Reasoning: Montana is great at being stealthy and having AA. Thus, you want to buff that. Potatoes think they have to buff the weaknesses of a ship. This is wrong. You want to buff the strength and play around the weaknesses by having better positioning etc. This buiild allows you to become untouchable to anything except unicum CV players and even then you will make them pay. It also allows you to stay safe at 15 km. Because if you stay at that range you become concealed after firing and waiting 20 seconds, meaning you can safely relocate if you need too.
2.
USS Missouri
Yes, I have her. Yes, I have a dedicated Missouri captain. No, I did not pay a single cent for her as I had freeXP saved up.
Tier 1: You could take preventive maintenance instead, but everybody hates Missouris and focuses them because they are jealous they don't have one. So it is good to know how many people are aiming at you. No catapult fighter skill because you don't have one - unless you trade radar for fighter in which case you should go play Iowa instead.
Tier 2: Em for turret rotation, Jack of All Trades and High Alert for faster heal and DCP (awesome combination). Adrenaline rush for better DPS in knife-fights and when you are low health. (You can get the reload down to almost 20 seconds if you are very low).
Tier 3: Basics of Suriviability (because everybody wants you dead) and SI for the extra heal.
Tier 4: CE for stealth. Same reasons as Montana. You could also go for Fire Prevention and drop Jack and High Alert for that. I don't
because I am not a pussy because I know how to control fires. I almost never die due to fires in my BBs, what I do die to is other BBs or torps. You got radar to see DDs, so less torps and Jack and HA is better for dealing with BB damage. So far Fire prevention is only good if you always bow on and always get HE-spammed.
3.
IJN BBs, including YAMATO
Tier 1: Catapult fighter, your turrets rarely break anyway.
Tier 2: Jack and EM. See above why.
Tier 3: Same as above
Tier 4: CE and AFT.
Out of all the Battleships, I think Yamato got buffed the most in this patch. Because you can now do an insanely survivable build like I did. Basically what I did was to trade manual secondaries and 2.3km of secondary gun range for Stealth (13.5km detection range on a YAMATO) and more survivability. This is a great tradeoff as nobody wants to come close to you anyway so you might just as well but everything into longrange firepower. Also, you still got pretty great secondaries even without manual control.
4. German BBs, including GROSSER KURFÜRST but excluding Bismarck, Scharnhorst and Tirpitz
Tier 1: Preventive Maintenance (DO equip Aux. Arm. Mod 1) and Catapult fighter
Tier 2: EM for turrets
Tier 3: SI for extra heal and EXTRA HYDRO (main selling point of SI over BoS)
Tier 4: CE, AFT and Manual Secondaries.
Reasoning: The Große Kurfürst is IMO the strongest Battleship in the game right now because she got a massive health pool. The Große Potatowurst is so tanky already that she does not need a lot of survivability - and stealth provides all the buffer she needs (see above Montana section on how to properly utilize stealth in a BB). Her awesome secondaries are the best in the game. You could switch CE for Manual AA to make the AA truly murderous, but I rarely die to carriers so I do not need it. Do not yolo in and think that you NEED TO USE THE SECONDARIES HERP DERP OH WAIT I AM DEAD WAAAH. Keep them for when you absolutely positively need to murder the DD that is camping in smoke 8 km away from you or for when that torpedo cruiser is typing ALOHA SNACKBAR in allchat and proceeds to yolocharge you.
5.
Bismarck
Same build as above, but switching Concealment for Manual AA (because more CVs need their planes murdered at T8 than at T10) and Expert Marksmen for Adrenaline Rush (your turrets already turn with cruiser speed, why you need more? Go buff main guns instead). Also priority target because getting focused while pushing is pretty nice to know.
I previously said that GK is the strongest BB in the game. That is true. But Bismarck is the best BB in the game right now, she is so much more fun than any other ship. She is so versatile and so tanky that you almost only want to play her.
6.
Scharnhorst and Tirpitz
Almost the same as the Bismarck build but using CE instead of secondaries as they don't have as many or as great secondaries.
I also got some specialized builds for BBs like Dunkirk, Texas, Arizona and Warspite but unless somebody requests them I won't take the trouble to write them up.
EDIT: Cruiser and DD specs to follow.