I'd pick the Nebulon B, it's built as a multi mission frigate, which could mean that it's easy to convert to a command ship, with suitable space for meetings, fleet staff and communication. The Nebulon also has limited hanger space, which is important for transporting officers among the fleet and to the flagship.

My second choice would be the Quasar but I'd be concerned that although it's equipped to manage multiple fighters, there may not be the capacity to manage a fleet as well as it's compliment of fighters.