From what I've seen, early on in Imperial Civil War, the team was having a lot trouble from Minor Fleet Commanders (i.e. spamming) and removed them. Since then, several others have asked for Fleet Commanders to return, but due to this problem they cannot return.
However, I present a solution: Minor Heroes. These heroes would be buildable from certain locations, and would be permadeath like the major heroes, and also would vary from era to era. This could solve the problem of fleet commanders, while also giving each era a little bit more diversity. Here is what I propose:
New Republic:
*Admiral Nammo & the Defiance (Era 1)-- the Defiance was an MC80 Home One-type Star Cruiser that served under the Mon Calamari Admiral Nammo's command from the time of the Battle of Yavin to Endor and afterwards, during the New Republic attacks on the Empire leading up Coruscant.
*Lieutenant Judder Page (Era 2)-- Lt. Judder Page was an Alliance SpecForce Commando with a penchant for destruction, and served during the Thrawn Campaign.
*Captain Genkal & the Naritus (Era 5)-- The Naritus was an MC80A Star Cruiser that has served with the New Republic since the days of the Alliance, and was utilized as an effective Fleet Command Cruiser as it searched for pirates in the Outer Rim.
Imperial Remnant:
*WIP