The official site has a new devlog available for wannabe ships' captains. Called "Captain Skill Training", here is some of what players can expect in the 1.2 update:
Speed Debuffs: Straight speed debuff skills can no longer be stacked. In many cases, they already couldn't stack, but we still let you fire off the skill and it didn't have any effect - so you just wasted the Morale points and got nothing for it. Now we don't let you use the skill unless it'll actually do something.
Crew Recovery: Many skills now add or reduce crew recovery rates. For example, the skills that increase the level of your boarding party all provide a passive crew recovery rate increase.
Buffs That Cancel: Several attack skills provide a small buff that gets canceled when you take damage. That's a pretty serious penalty and in multi-ship battles means you get little benefit since so many volleys are being exchanged. As a short-term change, we reduced the morale cost of these skills to make them more reasonably priced, and they're on our evaluation list for more significant changes in the future.
Now, on to the career-specific changes. I'm not going to list every skill that changed here, but I'll provide an overview of the majority.
There's lots more specific to certain classes of captains so be sure to head out.