The "Captain's Ability" is your ability to call in air support, ships, etc. This isn't present in the US campaign but can be (allegedly) modded in.
Crew Abilities are in both sides, as in crewmembers who have talents above and beyond the call of duty.
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"I wish to have no connection with any ship that does not sail fast. For I intend to go in harm's way." - Captain John Paul Jones, 16 November 1778, in a letter to le Ray de Chaumont.