Developers want a place to store app information that is critical and sometimes a very important part of the app(example main feature of instapaper is to view offline content). This should not be backed up since its redundant and when the phone needs to be restored(rarely) this data can be re-downloaded. Also backing up will be slow and destroy user experience.
Solution make another location which is used for storing the data(not backed up) so then all are happy. Maybe you can have data from hidden directories not backed up inside the Documents directory. Then Apple can delete caches in apps like browsers. User critical data like settings can be backed up and app critical data that need not be backed up can also exist