There's a whole batch of captain skill changes in 1.2. Offhand, I'd estimate half of the captain skills changed in one way or another. The vast majority of these changes are improvements to existing skills, and thus it impacts all careers.
First, there were a few global changes.
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.