Here's an update if anyone cares...
No, I didn't try the rsync idea because the migration itself is broken. The domain administrators are not transferred correctly - they don't have any privilege, but they should have at least "Create and manage mail accounts". I cannot manually change over 500 domain administrators.
Also, the migration is extremely slow - I tried migrating a mail-only domain with 870 users and it took more than 15 minutes only to create users in database without any actual mailboxes transferred. The transfer itself (about 8 GB of data) took 1:44h! Also the progress bar in migration is broken - it's stays at 50% for a loooong time, so it's basically unusable.
If I extrapolate this numbers, it would take 90 minutes only to migrate mail users without mailboxes and about 70 hours to transfer the mailboxes (we have more than 300 GB of them). Unfortunately there's no option to only transfer mail users without mailbox content so we could transfer that separately (this takes about 6 hours using 'native' rsync).
Another show stopper in Plesk 11 is the fact mail user has access to "File sharing" option when they login to panel. Why on earth would anyone want that for a MAIL USER? I also cannot see any option to disable this under roles or anywhere else and even if there is such an option, how would I change it for about 5000 users?? Another thing that is beyond my comprehension is why a mail user has all those options available in panel at all (Home, Mail, File Sharing, Account)? They only need options under "Mail" tab (vacation, forward, change password) and NOTHING else. This would surely cause a lot of confusion for users and unecessary support costs for us.
Not to mention that a plain mail user can see all account information under "Account" tab, like number of mailboxes, traffic, disk space used etc. etc. What were you thinking??
So basically, Parallels took a perfectly good (OK, there is always room for improvement) functioning panel version 9.5 and decided to make a totally new product which bares no resemblance whatsoever to the old product?
If you're trying to lose a customer who paid you thousands of dollars in 10 years of using Plesk, this is the perftect way of doing it.
In my opinion the correct way would be to keep the old panel line (9.x) supported in the future and develop radical new features in a different product (I don't care if you call it Plesk 15 or SMB or whatever), but I know this is not about to happen, so the only option I see is to migrate users to a different panel before June when your support for 9.5.4 ends.