On a side note: May I also point out that we already have at least two Fleet Admirals that I am aware of. Quinn and Akaar. (There may be more). So, perhaps Fleet Admiral is not the highest rank out there (as there should only be 1 5-star per branch and only during a time of war). Perhaps the CnC or Commander of Starfleet titles in Star Trek VI are actually a 6-star rank...just a thought.
Well, I think that Menn Hilo, the Bolian who gives you your rank-up ceremonies in ESD, might be Commander, Starfleet.
There is also Grigori Yanishev and Zav Glasch Trem (the poor Tellarite admiral who got one-shotted by a Jem'hader in Second Wave).
On top of that, T'nae, and Zelle are admirals, neither of whom I am sure on their rank, although Zelle doesn't matter of course.
See, I knew I missed some big Admirals. Also, to muddy this conversation up a bit more, I was watching some old TOS episodes and got to the Menagerie Part I only to hear "Fleet Captain Pike"; so I looked it up. Garth was also a Fleet Captain. While it is unclear whether or not this is a true rank or just a title, the term Fleet Captain does exist in the modern navy and, according to memory alpha was in the TNG officers manual as a 5-pip rank. Just kind of throwing that out there since STO seems to be focused on Fleets right now, perhaps another 5 level rank squeezed in between Captain and Rear Admiral, Lower?
One other point, if indeed lets say that there are to be only one Fleet Admiral per Quadrant, then there would still be a 6-star Admiral over all Quadrants. I look at it this way (this is just my opinion, not canon or navy related, just how I'd break it down in my head):
Rear Adm., Lower commands a task force; Rear Adm. Upper commands an armada: Vice Admiral commands a starbase/sector; Admiral commands a sector block/ a division of a fleet; Fleet Admiral commands a fleet. So that leaves two to three ranks above a 5 star Admiral; 6) Commands a group of fleets; 7) Commands a Quadrant; 8) Commands all of Starfleet (CnC).
Again, I realize that this isn't canon, however, if we use this idea to stretch the rank structure a bit it gives us a couple higher levels and dumbs down Fleet Admiral to make it not such an uber rank that having thousands is bizarre; it just implies that there are thousands of fleets to be commanded.
(I feel some heated counter-arguements brewing already...)
Real quick, the command of the fleet would go to the person who has been that rank the longest, that usually means the oldest, but there are sometime where that is not true.
Fleet captain has never been used by the U.S. NAVY.
Fleet Captain is the rank given to the Captain in charge of the ship the Admiral is on. So your first officer would be a Fleet Captain if this was used.
Commodore was used for those 2 people only, then Star Trek got rid of the rank, hence why people are rear Admiral Lower Half.