A lot of ideas, but here are some constructive suggestions.
JAG liasion - I prefer to have a junior JAG officer assigned as the ship's Legal Officer. He can do a lot of things including advising the CO on treaties and interstellar law and he can draft the treaties that Starfleet sends its ships out to negotiation.
Crewmaster - this one I stole from FASA Trek. He's a civilian relations officer who liases between the CO and the civilians on board larger ships...A tough administartion job.
Recreation Officer - the crew has to relax and nothing better than a Rec officer to make sure that they do. Working with the CMO/Counselor they make sure that the crew stress and morale levels remain high. Most are retired or semi-retired officers on the way out with fatherly ways to keep the crew relaxed. Some could be ordained ministers to keep the crew's spiritual well-being. I can see a Bajoran Vedek running the recreation department.
Intelligence - intelligence is strictly subordinated to tactical.
Communications - coms is also a tactical function as comms will relate to the ship's EW functions as well.
Flight Ops - i don't mean the Conn officer but the Air Boss, the chief of flight deck operations onboard Akira and El-Dorado class carriers. He will have to be an ex-fighter jock to rise to that post but he'll be transferred to command branch for that purpose. The flight deck crew itself would be Ops/Engineering personnel so would be the Boat Bay officer who is really a specialist in small craft operations.
Boarding officer - a mixed security/command function, the Boarding officer leads security/customs inspection teams to board merchant and other civilian ships for security/customs inspections. I think he should be command to give him authority to tell freighter captains where to stuff it...
One thing about the Watch Officer and the OOD.
The Watch Officer is the senior officer on the bridge during a duty shift so its usually the CO/XO or one of the senior staff.
The OOD (Officer of the Deck) is usually the junior officer working as the Watch Officer's right hand. Usually he has the "Conn" which means he runs the bridge under the watch officer's supervision, sort of an XO in training. When the ship is hard docked the OOD is in charge of the airlock detail making sure the right persons get on and off.
Arise, arise, Riders of Theoden!
Fell deed awake: fire and slaughter!
Spear shall be shaken, shields be splintered,
a sword-day, a red-day, ere the sun rises!
Ride now, ride now! Ride to Gondor!
Theoden King: The Return of the King