I've damned the new file system several times, but it isn't as bad as often discussed. The main problem is that there is no proper documentation and no guidance to find a good solution for an organization.
Lets look into the details.
Moodle 1.9. File handling is limited to courses. Each file has to be uploaded to each course where it should be used. Updating of files was not possible if the file was used inseveral courses. Other options were not offered by Moodle.
I hope you all can agree to this.
Moodle 2.0. I will start with a little guidance:
First step: Store all your files you want to use in your peronal file area. Ey, you can upload them as zip and unfold them in your file area. Please don't forget to save changes after uploading. Otherwise you will lose your files after some hours.
Second step: Go to your course, add a file as ressource, add a file to a folder, attach your file into an activity. Thats it. Not so complicate up to now.
Next step: You like to share files with colleagues in a course and reuse the file later in other courses . Create a folder in the course. All teachers can upload files. You want to download them? No problem. Zip them in the folder and download all files.
In this way you can do all the things you could do with Moodle 1.x, but you can reuse files without copying them. The main difference is: store files first in your personal file area.
Now the new features that were not offered by former versions of Moodle.
You like to offer a bundle of files that are offered by the organization. You are looking for an area where you can upload files centrally via FTP. Well create a folder called 'repository' in your Moodle-Data folder and define sensefull subfolders. Afterwards you can create a file server area in Plugin repository and give the system user reading access and option to use the files in the courses. Create FTP accounts for the folders and give access for the staff.
i think you can do the same with a WebDav system.
You've seen interesting pictures at an other webpage or you got an URL to a file you want to use in your course. Normally you have to donwload the file to your local PC and to upload it again. Now you do it in one step if you've activated the URL downloader repository. Add the URL of the page to extract the graphic files for your course or add the URL to a file to do the same for other formats.
You want to use files from public repositories like Wikimedia, Flickr, Picasa et al. Do it with the specialized repositories.
Now its getting a little bit more complicate. You are interested to use any type of external system where you store files. And you want to use not only a global account to all files for all teachers, but you also like to offer access for all private accounts from your staff. This is really much more complicate because an API is required for each system and the concept has to be supported by the other tool. This seams to be the point where the expectations and sometimes the phantasie is running high but Moodle can't fulfill the wishes in the moment.
Actually I only see one tool that connects Moodle user accounts directly with the user management froma repository system. This is the Alfresco integration developed by Remote Learner as part of the ELIS suite. Its available for 1.9 and will be offered for 2.0 in summer.
We are working with this suite and the features are great. The power of Alfresco document management system can be used if you configure the Alfresco system individually. But this is a complex project and not as easy as most people think.
Summarizing this, you can do all the things you did in Moodle 1.x, but you can do much more.
The Moodle repositories are far away for from being perfect, they have several bugs and I know half a dozen issues I didn't understand, but you can work with them.
Hope this descriptions helps to understand the system better. I'm also learning a lot while working with the system.
Main problem from my side is the missing documentation. Lets try to add the documentation asap.