Let's talk about that pesky Commodore rank. :)
It does seem that the rank has been phased out in Star Trek by the time of Picard & Co. On the other hand, Star Trek Online is free to "reimagine" some aspects of the Star Trek universe. Why can't we suppose that Commodores have made a triumphal return in this game?
No need for a "Fleet Captain" rank title, though. Blecch.
Let's look a little more closely at the Commodore rank. What is it they do, anyway?
The normal concept is that they don't exercise direct command over individual ships -- that's what captains are for. Commodores receive high-level tactical and operational information concerning an Area of Operations and then devise plans for forces of multiple ships to accomplish some appropriate goal in that AO. They'll then give operational orders to the captains of the ships in that task force or fleet as to what they want accomplished, but each captain is then responsible for the specific tactical actions their ship must perform to carry out that mission.
In essence the rank of "Commodore" is a special rank given to a senior Captain that provides some flag rank authority. A commodore will normally be billeted aboard the largest ship of a task force (which becomes the "flagship"), with physical space, staff, and equipment necessary to receive information, formulate plans, and communicate with the commanders of the task group. But doing this doesn't make him the master of that particular ship; the captain is still the captain.
In short, the commodore says what to do, and each captain decides how to do it. It's not entirely that simple, since a commodore may in some cases also give certain tactical direction, but this is a useful way to think of the relationship.
I could definitely see this working in Star Trek Online. I stubbornly persist in thinking that there's only going to be one rank of "Admiral" -- I just don't believe that a game developer will spend as much time creating features and content for a strategic-level game as they will on the usual tactical gameplay features and content -- but I think that still leaves room for a Commodore rank whose function is to command multiple ships for the really hardcore missions.