The thing you're missing though is that Apple has a solution for that, tags. And it's similar to the way playlists are handled in iTunes, how smart folders work in Mail.app, and how Gmail labels work. Using tags to group projects is actually better than using folders because they are more flexible. We've all had the situation where a file could be placed in multiple folders and you have to decide between them. With tags, that no longer is a problem.
If you notice, adding and editing tags is becoming more and more prominent throughout the Mac's interface with every major update. It's iOS that has been lagging a bit in this area. My guess is iOS 9 is going to fully embrace it. Remember, iCloud Drive is new. But I am certain this is where it's headed.