Having a member of the crew be a chaplain would be great as a the person in the crew who is the Captain's sounding board. Like Kirk and McCoy, Picard and Troi, Janeway and Tuvok.
In one of Diane Duane's novels, the duty of chaplain rotated among qualified crewmembers, in addition to their other duties. On a ship the size of the Enterprise Dee, I could see a full time chaplain, on smaller ships it might be more a part time thing. It would give you someone to talk too instead of the ship's councilor.