Well, it seems to me that the whole point of Linux packages is that everything is modular. You don't need to install all of, say, QT if you only need bits from one or two modules. Sure, it means that manually installing packages means installing dependencies as well, but the whole idea is to do it automaticly.
The advantage is you don't have much - if any - duplicated libraries or data. You have one copy, and its used by many things. This may not be very important on a Desktop or laptop where you have hundreds of GB to play with, but consider that on the N900 we only have 2.25GB -TOTAL- OS space, and the core sits in less than 256MB.

Also - ignoring dependency issues - on my Ubuntu desktop, there was a nice little DPKG-frontend that would let me double-click on a package and install it. No command-line, no nothing. It would even install dependencies, provided they were available.
Personally, I think deb packages are a great idea. Sure, there may be some issues repo-side; having people upgrade to the right versions etc... But those can be dealt with. And its better than Windows installation, for sure.