[eluser]CroNiX[/eluser]
I haven't used 2 separate application folders, but it seems they wouldn't be able to share any models/libraries/etc with each other since each has it's own separate structure and the only code they share is the base system dir. The docs mention each application would have it's own bootstrap file (index.php) and within that you define which "application" directory to use. I use some of the same models/libraries on both the frontend and backend, so want to use the same codebase for both and not separate them. Maybe your requirements are different, but you mentioned "bridges between them" which doesn't seem possible unless you want to duplicate some code in both applications.
If you are in application A and do $this->load->library('some_library'), it's going to load it from /application/a/libraries.
If you are in application B and do $this->load->library('some_library'), it's going to load it from /application/b/libraries.
Anything in application/blah/admin dir is enough separation for our design team which works on a fairly large complex national real estate site.
If you choose to go the separate application route, let us know how it goes. I'm curious how it would work and whether or not they can share models/libraries/etc between them.