For Windows users switching to Mac OS X, it's not really something they're used to doing. Instead of downloading an installer, clicking "Open" in the browser, and just following a guide leads to less issues with placing the application the correct place (Program Files), instead you get either a Zip file (so the bundle is in Downloads), an actual Installer (typically a .pkg), or a Disk Image which is often never unmounted. (I once saw a family member with 7 Flash Update disk images mounted)

As such, a lot of OS X users find themselves with a the Skype app in Desktop (inside a Disk Image), their Mail on the dock and some other app in Documents or Downloads. It requires that you organise it yourself.

Another way of saying it is that it lets you organize it yourself.

There will always be people who don't understand, or care to understand, how the system works. You can put in all the hand-holdy nonsense you want to cater to them and they'll still exist, but you'll be adding tedious and unnecessary hurdles in the workflow of people who do know what's going on.