This is now (sort of) possible by using Android Studio and Gradle.
Whilst subfolders are still not possible, it is possible to separate resources into different sets and have them merged by the build system.
As an example, to simplify my project, I wanted to keep theme specific drawables separate from standard drawables.
I created a new resource folder named 'res_lighttheme' as illustrated in the picture below.
I then added a pointer to this folder to my build.gradle file like this. To add more than one just add another line to the definition.
The result is that BOTH folders are then considered to be valid destinations for resources. A build error will be generated if there is a conflict. i.e if the same resource is included in both folders.
