This isn't a web service deficiency by Apple, it's a design choice for simplicity, which can be considered the most suitable form of file management for smartphones/tablets. For instance, instead of backing up bookmarks, my bookmarks are automatically synced to iCloud & across all my OS X & iOS devices. If I add a bookmark on one device, it's immediately available on all other devices. In addition, I see tabs open on all other devices from any device (desktop, tablet & smartphone). I don't need to manage bookmark files. This is a smart use of web services.
If you want to store & manually manage all your files online, there's DropBox et al as well as "hacks" to mount a folder in iCloud & use it like a network drive.