users could choose their own organization and/or hide languages they do not use
We can already have filetypes listed underneath the group menus, e.g. for custom filetypes that haven't set a group. We could support this for non-custom filetypes too. (Making all filetypes custom might not be possible if Geany uses the filetype enum IDs for special handling). This allows the user to make their common languages available from the first menu level. I don't think it's worth supporting custom filetype groups.