Not too long ago I characterised listening to such discussions like "listening to a discussion between a deaf and a blind man about whose condition is the easiest to live with". If people could just take a few steps back for a second, they would see that program management can be improved dramatically.
All of the points raised in the article are addressed in my Utopia of Program Management, a system designed from the ground-up for simplicity and ease-of-use, while also offering all the advanced functionality that power users have come to expect - and a whole lot more that none of the current systems offer. It offers centralised updating, the ability to effortlessly run multiple versions of the same program side-by-side (including multiple settings files), installation via repositories or Mac OS X-like bundles - whatever you prefer. You can manage your programs by hand, as on Mac OS X, or you can write an application like Synaptic and use repositories. Simple CLI tools are envisioned for command line junkies, but thanks to live queries, you could use the graphical file manager as well - no need for special tools if you don't want them.
Obviously, my proposal is just a solution. My point is that squabbling over today's methods is pointless - they all have their flaws and downsides which are very hard to fix without breaking the model anyway. What is needed is a dramatic re-thinking of how we manage programs and applications, instead of wasting all this energy on these pointless discussions about Linux vs. Mac OS X vs. Windows. We could do so much more with technology available to us today.
Program management is probably my number one frustration in managing operating systems today. Sadly, I'm not a programmer nor am I anyone with any power, so all I can do is highlight the problem, and make sure people know about my alternative plan that is far superior to anything any current operating system has to offer.
I fully understand that you can't change the world overnight, but it's pretty obvious that no one seems even remotely interested in breaking the status quo, as we're far too busy with "my dad can beat up your dad!"-discussions; and that in an industry which is built on fast development and the rapid adoption of new technology. It's appalling.