Do you consider it a design weakness/limitation that all other libraries are one level deep under QSYS? QSYS is the only library that can contain other libraries. This is by IBM's design.
If you want to mimic the structure of other libraries nested within libraries, e.g. QTEMP, SECURITY, PRODATA, PRODCOMMON, CUSTOMOBJ, PRISTINEOBJ, QGPL, just use library lists. The library list provides that capability, up to 250 libraries in a list.
Specify one list of libraries for production, another list of libraries for Test, another list of libraries for Development.
Many single-LPAR machines provide Production, Test, and Development environments by using different library lists.
If IBM's design of QSYS and its child libraries is a limitation, what examples of application software providers can you point to that have said, "we gotta have libraries nested within libraries and therefore we choose [name-the-operating-system-and-database]