Flag - Provides staff level interaction with greater access to Intel and more delegation of duties.
VS
Command - Provides command level interaction with more hands-on shipboard-centered play and less delegation of duties.
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COMDESRON vs Command-at-Sea
Commodore vs Captain
DESRON vs Command
CIC vs Bridge
Crew vs Command
Staff vs Command
Operations Officer vs Captain
I guess it depends on how you want to look at it. The thing to avoid is making players feel diminished if they choose the more simplified mode.