Icons on the desktop:
Finder > Preferences > Show these items on the Desktop
This is the first thing I do when setting up my user account on a new OS X system. I too like my desktop clean, and it's quite simple.
I use Virtue. Probably didn't exist at the time you were making up your mind, though, from the sound of the article. Even if you were to try it today, it may not meet your expectations depending on what you're used to in Linux; I find it does exactly what I need.
Focus follows mouse:
Can't help you there. I personally hate focus follows mouse, so I've never gone looking for a way to implement it.
I use DarwinPorts. Works great for me. YMMV.
First-class package manager:
Though I use DarwinPorts for UNIX-based apps, I don't get how having a package manager put things in its own hardcoded locations (which vary from distro to distro) is supposed to be more flexible and user-adapting than letting me drag the app icon wherever I want. The most annoying apps on OS X to me are the ones that force a location on me. It seems strangely out of place with your philosophy of customization.
Downloading files to the Desktop:
The location for downloadable files can be set in the web browser, same as web browsers on any platform.
Most apps log errors/status to the console.log file. You can view this from the command line if you like, but /Applications/Console will show the log files on the system and has a rather handy filter box. As for more detailed information on what the app is doing, Apple includes tools like Shark and Spin Control that will provide that in a nice way.
Lack of freedom:
I don't see how you having to adapt to the system follows from being able to see the source code for Mail.app. I find Linux to require far more adapting than OS X (the old "...it's just picky about it's friends" line). Guess it just depends on what you're used to.
Because having two files named Readme and README is just plain stupid. Still, a case-sensitive variant of HFS+ is now included in OS X as an option (but was probably added after you made up your mind). I have never run into a need for it, though, and I use quite a bit of open-source software.
Classic UNIX utilities and resource forks:
They do as of 10.4, which sounds like it came out after you'd already decided to switch back to Linux.
I don't mind paying people for work. Sometimes the open source apps are good enough, but I've seen many projects abandoned because people have to make a living somehow, and I don't have the time to write code for every single project that's useful to me. I do use Spotlight, and things like the Kerberos integration in 10.4 make it well worth paying someone to do for me. I'm not sure how GarageBand fits in here as it's not part of the OS.
I think your main valid points here are:
- you like the fuzzy feeling of having access to the source code, even if you never use it
- you don't have any need for software that OS X does really well (e.g. media apps)
- you're used to the way Linux works and don't want to change
These are all perfectly fair points, and valid reasons for you to use Linux instead of OS X. But I didn't find the rest of the article to be as informative. Some of it's due to advances that have been made since you switched back, so I can hardly fault you for those, but some of your complaints about lack of customization are simply due to not even looking (e.g. Desktop icons). I'm not sure I agree that you gave it a fair trial. But as I said, I still think you have valid reasons for switching back.