I agree completely about your opinion, Gustav. Maintaining two separated threads of coding is really difficult, more if such threads affect core features like the backup/restore.
But, thinking in future applications for individual activities (not only backup and restore in its current approach, but sharing them using a lot of alternative ways like web-services
And all this will break backup/restore as it's currently implemented and will force us to maintain two lines of code, exactly like the quiz restore is being supported now.
So, why not to start by creating and designing all those new XML stuff without the constraints of current backup code, leaving it to follow its own development cycle and, once all the new XML architecture is created use it to build the new, improved, 2.0 version of backup and restore.
With this, old courses could be restored without problems, because such line of development has continued active and independent. And starting in versión 2.x of Moodle we could start to create 2.0 backup files (with its own structure and code).
I must remark that all these are absolutely preliminary ideas and I'm pretty sure that every alternative has advantages and handicaps, but I think we shouldn't avoid the "separate completely" alternative yet.
Perhaps, once defined the objectives of the whole thing, we could decide the best road map to fulfil it, but not before (pop*, of course).
Ciao
*pop: personal opinion