You can already do that. Just uncheck copy on import or whatever the wording is in the iTunes preferences is (under advanced) and you can just store things on different drives.
I think the point would be to let iTunes still manage the files, but to have control over the layout. You can absolutely do what you suggest, but then you are still responsible for managing the files. (Granted, some folks might see that as a "plus".)
There's also the more general issue of the "filesystem-less filesystem" design that Apple seems to be migrating to. The typical user really doesn't care where each individual "file" is, as long as they can access it when they want, via whatever application they want to use*. Administrators, though, will want the ability to specify where certain files or file types go, especially in the case of multiple disks, NAS, cloud, etc., in the environment; the objective would be to allow this level of control, transparent to the typical user, and still allow the OS to manage as much automatically as possible.
Back to iTunes-specific stuff, I think greater support for the multi-user (family) model is a really big issue. To truly adopt the whole Apple "ecosystem", they need to make it easier to have a central iTunes library that be can accessed by multiple users and from multiple devices, and make managing and updating the library a much less manual and error-prone process.
To wit: my iTunes library lives on an NAS, but I have two computers that access the library and a total of four user accounts between the two computers (one is the same on both). As it stands currently, if I change a file type (say, from "Music" to "Audiobook") in one account, it "breaks" the other three because iTunes "manages" the files and moves them to a new location. Similarly, if I add new content to the library, I have to manually re-scan the library from the other accounts to see it (which can be a real pain if I'm trying to screen out certain music/video from the kids' account) - I would have this problem even without iTunes "management" that causes the previous issue (which can be worked around by turning "management" off and manually managing the files).
What would be much nicer is if iTunes treated its library more like an actual database, and used database syncing technology to keep multiple accounts on the same library in sync with library updates, while still allowing individual accounts to keep their own playlists, play counts, ratings, etc., distinct from each other.
Also, and this isn't really an OS or even application issue, for the love of Turing, please allow us to merge items purchased under different Apple IDs into a single ID!
--
* Edited to add: Of course, even a "typical user" may want to allocate which files/file types/groupings/etc. live where in the case of having, say, a MacBook hooking up to an NAS -- you want to be able to specify which content should stay on the notebook for when you're away from the NAS, for example.