I'm going through the same thing with my first Amiga, only the packages are much smaller. ;-)
Linux is a bit extreme, and there is only one way to get around it: avoid applications which incorporate too many features. For example, mutt and pine are good email readers. Yet a lot of people ignore them because they are character based applications and don't allow you to view formatting or embedded graphics. But a GUI would require widgets (gtk+ and qt are the popular widget libraries these days), formatting may require an HTML parser (which may be provided by another library), and the ability to view images will require more code (typically provided by the jpeg, png, tiff, etc. libraries). No Linux programmer wants to develop all of that code on their own, so they grab what is available.
Another problem is competition between libraries. For example: gtk+, motif, and qt are just three libraries which provide widgets. There are many others too. Motif wasn't free (as in cost or liberty) originally, so people looked to qt. While qt was free in cost, the license didn't offer much freedom. But the widget library was nice and comprehensive, so some people used it. Other developers wanted a free (as in GPL) widget library, so gtk+ came into being. The other widget libraries were largely developed to suit other needs, such as the desire to avoid bloated widget libraries.
As I suggested earlier, you can avoid a lot of the problems by choosing your software carefully. It is part of the culture of Unix, and one of the reasons why I think Unix will never catch on among people who don't appreciate the many details of their system, or the choice it provides. Is it a waste of time? Maybe to some, but it isn't in my opinion. Then again, I'm spending a considerable amount of time to get a 68k Amiga to work. :insane:
