Hi Tim,
The new file API was designed and implemented to fix a lot of problems we were experiencing.
As one example, you say you'd like to store files on disk using their original names. This single requirement would mean that many of our users would experience huge problems (as they did in Moodle 1.x), since they want to name their files using all kinds of non-latin characters, and many operating systems do not support these well. Talk with people trying to use Moodle in Japan, for example.
Another old problem is that we could never tell what files were being used by exactly what activity. This led to all kinds of issues with backups, security, images appearing to teachers but not students, and so on. For example, if you wanted to backup one Forum you had to include EVERY file in the course, which could be gigabytes. Course import often broke, too, because we did not know what files to bring over with
activities.
Following from this, every file in the course files area had to be readable by students (because we had no idea where/how they were seeing it), so a smart student could easily guess URLs and gain access to all kinds of files that teachers thought was private (and thus cheat).
The answer is not to go back to the 1.x design - it's too late for that. If there are issues with the 2.x interface then let's work on them (as we have been for over 2 years). One of the things that was always planned (though sadly not finished yet) was a
WebDAV interface (built on top of the File API) to make it easier to drag files in and out of Moodle. There is also the filesystem repository and a new course files repository that mimics a lot of the old behaviour for those who really want it.
To me it's clear that the general trend in the world is to move towards specialised repositories that do that job really well, and then plug these into application servers like Moodle to use the files.
I think most of us involved recognise that there is going to be some re-learning required, that old workflows may have to change, but the result is a more powerful, flexible and international tool with fewer problems.
Finally, Moodle 1.9 is still around. If you can't adapt your custom backend stuff then you may not want to upgrade, and that's fair enough.
Cheers,
Martin