Currently our existing Android projects have the old Android Project structure created by default, even for new projects, which makes no sense since we no longer support Eclipse as the default project editor and have moved to Android Studio for Android development.
The main reason for doing this is to clean up dependencies and to allow for projects and dependencies to work more like how modern Android projects work and to remove as much custom Gradle code as possible. This would also allow us in the future to move towards having Android Plugin code work as Android Libraries with Resources instead of just copying things across, which gives us the ability to add JUnit tests and bundled resources. This would dramatically increase the quality of plugins such as InAppBrowser, and third party plugins such as the Barcode Scanner.
This would have to be done on the next major version, and the upgrade would be tricky to do. However, the benefits at this point would greatly outweigh the costs of maintaining the old project structure. The old cordova-common code in Cordova-Android 5.0.x would allow for plugins in the short term to work with both projects until we get the new project structure ready.