But maybe do a thought experiment sometime about “What if I kept my game objects separate from my scene objects?”
You lose almost nothing.
You gain tremendous flexibility and a nice separation between game logic and view logic.
You also gain the ability to ignore JME’s broken serialization mechanisms, accidentally saving a bunch of stuff not needed by the game object (meshes, materials, etc.). Suddenly, any other standard Java serialization will work. JAXB for XML, Google’s GSON for JSON… even Java’s own serialization can work.
It does mean that you have to ignore most of the simple examples in the tutorials.