Drawbacks with the Projects approach include:
- The project (i.e. "folder") in which a repo resides isn't
usually visible, for example in the Homepage or your Profile. To make this visible in those places would require a manual tag in the repo's name, for
example like @peter554 suggests. But then changing the "folder" (i.e. project) requires
changing both the project and the manual tag in the repo's name.
- You cannot add forks to a project.
These problems are not present with the Organizations approach. However:
- Your "foldered" repos will disappear from your account profile page. But organisations can be made visible there by becoming a public member. (can be set under "people" within organizations)