1) This behavior is intentional. It’s about exporting multiple sub-meshes which should have right position/rotation/scale in relation to each other.
2) You can export multiple objects as sub-meshes. The purpose of the mesh export plugin is not to build a level in Blender! You don’t need to automatically export every sub-mesh in a new file for building 3D objects to use in your game. Simply create a new Blender project for each new object.
3) is similar to 2): It is not the purpose of the Blender plugin to allow you building levels in Blender! It is just a way to import meshes made in Blender into the native level editor!
I don’t think that any of these are really bugs or problems. The Blender plugin does exactly what it was meant for: Exporting meshes from Blender!
Sorry if I sound too harsh. I don’t want offend you 😀
Things that really need to be fixed are problems with newer Blender versions concerning valid output of materials, animations and geometry. Since Blender likes to change the plugin API a lot it needs to be fixed regularly.