EDIT: Seriously though. People are making a big deal out of someone having a different opinion. Silly.
> 'one window' = 'one application' is a fallacy
> hate clicking on Terminal and having something new pop up when I might just be trying to bring that application back into focus
Aren't those conflicting statements? The latter only occurs when the former is not considered a fallacy, no?
So clicking on the application icon will present the user with all documents opened by this application, hence will raise all of its windows, while modifier+clicking will create a new document.
This has really annoying consequences in OS X where it trips me up all the time. For example, I open a pdf from within Safari. I finish reading and close it. I expect to be back in Safari: I'm not; I'm focused instead on a completely unrelated photograph that I'd opened ages ago and forgotten about.
Linux GUIs were traditionally all about documents. As they've tried to converge with Mac and Windows, they've become more about apps. IMO that's a shame, but there it is.
That said, there is plenty of other questioning that can arise like, does one close the application when all windows are gone? Tricky.
Mac made a huge all-breaking change with Mac OS X. That only occurs every few years, but as you say, Gnome 2 is ten years old. Then Lion introduced all kinds of workflow-breaking changes, like the automatic spelling correction, the "overview mode" or whatever it's called, the reversed scrolling. And you have to suck it up that much more on Mac OS, because there's just no way to install a different version of the interface.