I've only just recently started migrating to Debian. The packaging system seems to be both powerful and user hostile at the same time.
For a start everything is still firmly rooted in the commandline. There are programs like aptitude that try to hide some of this but it seems pretty obvious that this stuff was designed for commandline users.
The other thing that struck me is how many dependencies I need to bring down just to update one package. Sometimes I'll do an update and get 50 other packages along with it. Some of these seem to have nothing to do with the one I actually wanted.
The windows packaging system may have a lot of technical problems but at least it's easy to comprehend. You download one bundle. Run it and everything you need is bundled.