When planning to use file referencing in your production environment, consider your team’s workflow practices (modelers, riggers, animators, materials and so on), as well as the overall requirements for the project before you determine your scene’s hierarchy.
In general, you should reference files in a bottom up manner (that is, reference small items into bigger items). This bottom up structure allows you to easily load or unload any segments of the scene that are not required by the user. For example, when creating a city parent scene, a door and other related components should first be referenced into a building file. Then reference the building into the street file, and then reference the street file into the city parent scene.
When building a character, reference the model into the rigged file. Then reference the rigged file into the environment where the character will be animated. This ensures that a change to the rig is correctly propagated to all environment files that may use the character.