Is everybody that uses iCloud working on perfectly manageable one file projects? Im not. My projects have drafts, excel sheets, images, videos, PDFs, Word documents, etc. I need to keep those files together, as they are the project.
With iCloud I simply cannot do that. I have to distribute my project files over every single app I need to use to manipulate my project. As a trade-off, if I want to use iWork in the Cloud, I need to duplicate my files, edit/sync them, and then afterwards regroup them in a folder on my Mac. Its madness.
The biggest issue is that Apple forces its hidden-file idea on you without giving a choice. Offer it as a solution for newbies, for cooking recipes and party invitations, but for serious work, give us a file system. Its been around for 30+ years, theres nothing wrong with it.
Yup, iCloud doesn't work that way.
You want to keep different types of files together based on their content.
Apple believes this system is too difficult for beginners. People like you or I can work with it just fine, but lots of people don't really get to grips with the filesystem. Lots of studies have pointed to understanding the filesystem as the point where people who "can use" a computer become people who are really comfortable with a computer.
Personally, I agree that Apple is looking at the right problem, but I think they're trying to solve it in the wrong way. "Every App is an island" can work for some types of read-only data (like music), but for data which you edit it becomes too restrictive. Apple already had to build an exception to that rule for Photos, but they seemed to have glossed over thinking philosophically about why they had to build that exception and what it means for their theory that the App should manage all of its documents.