First, hope your 2 version is 2.4 and not 2.5 dev (development). ;)
Yes, there is a way that is similar to the process in 1.9 ... using 2's File System repositories. Turn them on. That creates a 'repository' directory in the data folder. Moodle will not create directories in the repo. System Admin has to create them manually and set appropriate permissions. Those could be your samba shares as in your 1.9's.
The 1.9's that cannot be backed up ... do they fail at creating the zip or copying the zip? Check the 1.9's data folder ... temp/backup/ directory. You might find zips that are too large to copy - but NOT to large to move to another location on same server or 'scp' to another server.
Example (one way ... am sure others might have/use different methods):
1.9 course ID 6 is one of those large courses. In the 2 Moodle repo, create a directory called '6'. On the 1.9 server from the terminal as root user and in the '6' directory, issue the following:
scp * root@newserver:/path/to/mdl2/repo/6/
This would copy everything in 6 on the 1.9 server to the 6 repo on the 2 system. Have to change ownerships/permissions on the files in the 2 repo 6 so Moodle can use see, but they are all there!
Then, in the version 2 course that had those files, create a file system repo and point the repo to the 6 folder. Teacher can then relink without having to upload.
'spirit of sharing', Ken