I concur with your users on all points, especially the package deltas. I would like to see a better way of managing packages (or uploads) in general so that users can easily add, update, and delete packages from the BES server. Also, removing the 2GB limit on the software distribution wizard would save us a lot of headaches.
FYI, you can mimic a copy with overwrite ability by using the delete command in actionscript before using the copy command. If the file is there, it will be deleted. If the file is not there, the delete command will fail, but the action will continue anyway (unlike when using the copy command on a file that already exists).
for the deltas, what prompted the issue is level setting the office environment. Having to tweak a single file in a 900 Mb package multiple times and then uploading it is not fun. For the delete command, yes that is what our user group is doing but it is annoying.