The way iOS works right now, apps can't handle this on their own.
Say I have a project. I have the budget in Excel, presentations in PowerPoint, and documents in Word. On iOS, each file is saved inside the respective app. If I want to keep all the related files in one folder, the only solution is to save them in the cloud, like on DropBox or OneDrive. You may have a point that metered Internet isn't really a problem, but there are other reasons why people might not have a constant Internet connection. For instance, I spend a lot of time on the subway, where there is no Internet.
Don't get me wrong, I love iOS, and most of the time, I'm content to work around its limitations, because for me the benefits outweigh the inconvenience. But let's not pretend there is no limitations. Exposing the entire file system like with jailbreak isn't the answer, but Apple needs to figure this out at some point.