Fascinating analisys, Penta! I was actually thinking about the same things and our conclusions are remarkably similar. I guess that means our basic principles are sound. A few notes, though:
First, a cosmetic thing. I'd try as much as possible to avoid duplicating specific real-life US Navy terminology, and stick to what we see on screen or try to think up something new or more universal. Starfleet should be recognizable as an organization to us but we shouldn't forget it's supposed to be a military of a hundred different species.
So I'd drop the Bureau thing and simply use Starfleet Medical, Starfleet Security etc. If we really need to use something, I'd choose 'command'. It sounds more universal and modern to me, we have precedent with Starfleet Command and SF Materiel Supply Command (from the DS9 Technical Manual) and it shortens more logically (Starfleet Medical (Command)). In fact, today's Navy has transformed most of it's bureaus to commands.
Fleets should also be 'First', 'Second' etc. as seen on DS9. 'Sectors' are also often mentioned so they should probably used as well, maybe instead of Districts or SFOAs.
As for the bureaus/commands:
I mostly agree with you. Maybe Construction could be split to Ships and Installations. SCE could be a separate 'operational' command doing (among other things) the field work for Installations, which would handle planning and managing. Kind of like how in the US Army you have both a CoE and a separate Installation Managment Command.
I'd add the above-mentioned Materiel Supply Command. Maybe an Equipment Command (though MSC could do that as well) which could also deal with weapons (though the reasoning for a separate bureau is also sound). I don't think Reactors is needed, Ships could handle that. I'm not sure where to put SF Communications...
One more thing. I do believe there are ground forces (though limited) and I think they would deserve a separate command - Starfleet Ground Forces Command - or better Planetary Forces, since it should include (atmospheric) Air Forces supporting the ground units as well. I'm not clear whether this would constitute part of the OF or the Shore Est.
3. I am very conflicted as to whether Starfleet Academy makes up the main or even the predominant accession source for Starfleet officers...
I see it this way: San Francisco is only the main campus, with other campuses all over the UFP. After all, the Federation is huge, it wouldn't really be practical to ship ALL the cadets to a single location.
OCS, direct comissions training (Troi got her education at the University of Betased, I think) and maybe even some enlisted training ('Chief Petty Oficer academy') could also be handled by SFA, explaining why almost all officers talk about 'the Academy', as well as O'Brien's temporal mechanics classes.
4. I'm wondering: Does anybody else see Starfleet as having a significant reserve force?
Yeah, it's only sensible that there's a Reserve. But, as has been already mentioned, we shouldn't forget member state forces - it seems logical that they are the ones mostly dealing with on-the-surface and in-system matters. So you'd need a 'National Guard bureau' as well, to oversee their training and organization so as to ensure their interoperability with Starfleet, especially if they get federalized.
Again, I would try to think up a new name (they're not exactly national, are they?). Maybe Home Forces? I can't think of anything better now. Of course, that would just be the common designator, I'm sure they would be allowed to keep their old names - we would still have the Andorian Imperial Guard or the Bajoran Militia, for example.
I have a few thoughts about the Operating Forces as well, but I'll post them once I make them a bit more coherent.