Package builder works well but there would be two features that would make users life easier when transitioning from other packages. The first would be the ability to package (ie custom format) documents. Eg. On a company site or site involving employment, the ability to package a application form, financial details form, application checklist etc. At present I have to combine in a single pdf package. Likewise on a church website, marraige form, guidelines, booking sheet and sample booklet.
Custom package types are planned. So for example instead of packaging a Joomla installer it could just package the selected into a zip file.
Second feature would be some form of drag and drop. I upload files via ftp and then configure. For superusers this is fine, but at the user end the ability to select the directory you want it in, and then upload into it and automatically create the path would be good.
Uploading is tied to the package. They don't select a directory, but select a package to upload files to. If versioning is used the Files page for a package supports drag and drop. It is not a file manager so it's never going to have functionality to manage files in such a way.