The existence of these projects is necessitated because users want to use unix-y programs but they don't know how to compile themselves. I don't use either of homebrew or macports anymore. I used to have them but then when I want to make something that depends on something I got from homebrew or macports it doesn't quite work and I end up downloading the source and compiling it into a framework using XCode myself anyway.
I've done this so many times it doesn't take me more than a few minutes to get all the dependencies in order. (I can re-use frameworks I've made before). The frameworks are embedded into the application bundle and can be used on any other computer that can run universal binaries. That makes the app portable, too. The beauty of all this is that other computers don't even need a compiler installed and they can still use the same programs I built. Of course it'll never beat apt... but it's the easiest in terms of getting that DVD to ipod video converter onto my aunt's computer.
I believe you're right. If you want package management the OS has to be built around it, otherwise it won't work quite right (unless you put time into it, of course).
I still will use macosx though, it needs less configuration and everything just works; or maybe I'm just too used to it to use anything else. Mac OS X is built for consumers and developers who develop for consumers who use Apple products. For these consumers and developers Mac OS X is the best there is. Unfortunately I think that's it. Terminal is still good, though.
To upgrade your OS, you only need to click "Restart" when software update tells you to. The only time you need the DVDs is when there is a major version out, i.e "Leopard", "Snow Leopard", etc.