One concept I've been thinking about for my os, and in particular my file system, was having multiple virtual filesystems on one physical one.
The idea exactly would be a new structure, the file system entry point list, defining a list of names and associated inodes, including the quota for those partitions. This would allow a sysadmin to give every user his own virtual "home disk" called home, without actually partitioning off 50MB for that user. It would allow dynamic resizing of virtual partitions, a system partition only the system itself could modify (and the user could modify only indirectly) and, one idea I liked a lot, a separate partition where all the files for a specific application are stored, together with its dependencies on other applications. This would allow you to make an application that uses a number of dynamic libraries for the application in specific, and a number of libraries for general use, and put them in two different locations altogether, thereby fully avoiding any mix of files, any sort of chaos (look in windows/system32 or /lib to see what I mean) and a number of lingering directories, save files and things like that (your program files or /usr directory).
A second idea would be to give each user on his or her own home site a configurable view on the computer disks. The user can set how he / she wishes to view the system, and what things should be used.
This allows the system to have a different directory structure for each user.
One of the final ideas I like a lot is the option to have the home site not on the harddisk of the user, but on an internet server somewhere. This would allow all users to make adjustments to their environment, and would allow them to work at any computer running my OS, with their own files and settings (limited as by the physical computer they're using).
And, because I'm not one of the "good guys", I'm not planning on giving my OS away for free, the space rental is a point of profit, as is the user usage limit. A user would buy for instance the 2-month right to use the OS on his/her computer with a specified set of programs, for which he/she would not pay the full quotum, but only the small portion he/she actually uses. This allows all users to test all applications you want to test (you buy the use for 2 hours / 1 day / 3 years, you decide), be as up to date as you want to be (within bounds, 1980 software might not be available anymore) and to use any computer you might find as your own. The downside would be that each user would have to pay at a fixed rate for a single service, that other providers offer for lower tariffs.
HTH, and if you are one of the good guys, ignore that last bit