Given how things go in STO, the rank structure for the Federation doesn't make any sense. It would if it was applied to the U.S. Navy. However the overall rank structure for STO is a bit off, this is mainly for the upper echelon of ranks. But we will start at the lower ranks and work up, including the changes that would have the rank system make more sense.
O-2 Lieutenant Junior Grade
O-4 Lieutenant Commander
O-7 Rear Admiral
This is removing the Rear Admiral, Lower Half Rank and drop in grade.
O-8 Vice Admiral
Just a Drop in Grade.
O-9 Fleet Admiral
Makes no sense that someone that is just in charge of a Fleet is the highest rank. So a drop in grade.
O-11 Admiral of the Quadrant
Can also be used for Admiral of Starfleet. By Navy Rank, this is Fleet Admiral. But this rank was created for four people to use in 1944. It hasn't been authorized since. But since Gene Roddenberry based Starfleet off of the Coast Guard and not the Navy. That means Admiral is the highest rank one can obtain.
This is how I see the basic setup of the rank. But, since a player can't be an 0-11 in this structure, and that we have up to 5 Pips(or stars), it would have to go more like this.
O-7 Rear Admiral, Lower Half
Commodore is still a listed TNG rank as of 2366, there is no supporting evidence here that the rank has been deactivated. So the player can choose to be referred to as a Commodore here. It just won't be the actual rank for the level system.
O-8 Rear Admiral
O-9 Vice Admiral
O-10 Fleet Admiral
This way the parts to the Admiral rank, which are namely titles, are out of the players reach. Examples being, Admiral of the Quadrant or Admiral of Starfleet.
This also returns it to a more Coast Guard like rank structure. Though, they only have O-10 as the highest grade, Fleet Admiral isn't a rank for them. So it just re-organizes the two highest ranks.
Though for how Starfleet works. The following could also be used.
O-8 Rear Admiral, Lower Half
O-9 Rear Admiral
O-10 Vice Admiral
O-11 Admiral or Fleet Admiral
This puts the Admiral and Fleet Admiral on even footing. Which title they used would be based on what their station was. Admirals would be the ones at Head Quarters, Starbases, and Ground Installations. The Fleet Admiral would be the ones out commanding the fleets. This also puts the Vice Admiral rank in the position to be either an Admiral or Fleet Admiral.
Before you say anything about the Commodore rank, yes, it is still an active rank for many of the world's militaries. The Coast Guard still uses it as an active rank for the civilian volunteers that hold an office with them, i.e. District Commodore.