The hard part for every one, what slots to choose.
This is what i have figure out from reading blogs and game experience.
Auto-Heal, Bind-Resistance, Despair-Resistance, Slot Rate Boost and for the last one I will say Damage Reduction or Charge Specials.
Whitebeard
The only unit (for now) that should never have Auto-Heal to make it easy for you to control it's captain ability.
4 Slot Units
Auto-Heal, Bind-Resistance, Despair-Resistance, Slot Rate Boost
3 Slot Units
Bind-Resistance, Despair-Resistance, Slot Rate Boost
2 Slot Units
Bind-Resistance, Slot Rate Boost
Now, why Bind and not Despair?
With Despair you can still use specials, so if you have Bind or Despair reduction you can use those specials and release the units.
1 Slot Units
Slot Rate Boost
How to measure slots?
Sum the number you have on each unit of your team and you will know the level for that skill.
And yes it will sum also with friend captain slots.
Why not Map Damage or Poison resistance?
It's easy to counter those 2 if you have Auto-Heal and in maps you don't take Map Damage or Poison you can always use Auto-Heal for stall, or even if you miss those sweet perfects.
Explanation of the slots and their levels.
Map Damage Resistance
Lvl 1 - 10 points, Reduces damage from Map Effects by 50%.
Lvl 2 - 20 points, Makes crew immune to damage from Map Effects.
Poison Resistance
Lvl 1 - 10 points, Reduces damage from poison by 20%.
Lvl 2 - 15 points, Reduces damage from poison by 50%.
Lvl 3 - 20 points, Makes crew immune to damage from poisons.
Chance to Survive
Lvl 1 - 5 points, Tiny chance to survive an attack with 1 HP.
Lvl 2 - 10 points, Small chance to survive an attack with 1 HP.
Lvl 3 - 20 points, Occasionally survive an attack with 1 HP.
If it worked like the mobs we face it would be something to consider, but the chances are so low that it's best to spend those slots in something usefull.
Charge Specials
Lvl 1 - 10 points, Reduces Special charge by 1 turn at quest start.
Lvl 2 - 20 points, Reduces Special charge by 2 turns at quest start.
Don't get me wrong in this one, it's an interesting boost but at max it lowers cooldown by 2.
This skill would be the one i would consider to replace damage reduction.
RCV Boost
Lvl 1 - 5 points, boosts crew's RCV by 100.
Lvl 2 - 8 points, boosts crew's RCV by 200.
Lvl 3 - 12 points, boosts crew's RCV by 300.
Lvl 4 - 16 points, boosts crew's RCV by 500.
Lvl 5 - 24 points, boosts crew's RCV by 1000.
Bind Resistance
Lvl 1 - 10 points, Reduces Bind duration by 1.
Lvl 2 - 15 points, Reduces Bind duration by 2.
Lvl 3 - 20 points, Reduces Bind duration by 3.
Despair
Lvl 1 - 10 points, Reduces Despair duration by 1.
Lvl 2 - 15 points, Reduces Despair duration by 2.
Lvl 3 - 20 points, Reduces Despair duration by 3.
Auto-Heal
Lvl 1 - 5 points, Heals crew by 100 HP at end of turn.
Lvl 2 - 8 points, Heals crew by 200 HP at end of turn.
Lvl 3 - 12 points, Heals crew by 300 HP at end of turn.
Lvl 4 - 16 points, Heals crew by 500 HP at end of turn.
Lvl 5 - 24 points, Heals crew by 1000 HP at end of turn.