graceful autosave points, in that the 'restart' command restarts only the current bsp, as opposed to the entire hub (which is what would happen if you had only a single bsp). There are other methods of course, but this is the more intutive solution for that...
can run on public coop servers without requiring clientside extensions (and can still work in vanilla servers too, but with the caveat that it ends up somewhat like prydon gate's 'hub' stuff if you're take care over 'startspot' not being transfered).
lower ram use (bsps don't have to be loaded in their entirety, ents can potentially be zipped saved to disk between maps).
less active entities at one time (relevent if you use ode or gyro or other cpu-intensive qc stuff).
clearer demarkation of areas.
keeps the mapper aware of just how much backtracking they're forcing the player to do... I hate backtracking.
shorter individual compile times.

I'd state the disadvantages, but:
a) I'm lazy.
b) you didn't ask for those.

.