Herein lies the problem. The term "better" is most definitely subjective.
Not to pic on Xcode, but this is a prime example of focusing too much on making a consumer appliance rather than a professional tool. Like I said: I don't want iTunes, I want a kick-ass IDE.
I'm in the middle of a project that has, quite literally, thousands of assets to manage (images, audio, video). The thousands of files end-up piled-up without any semblance of organization in the project directory. I mean, who woke up one day and though "This is a good idea!" when you have a perfectly good file system to take advantage of? Updating assets is an absolute nightmare.
Yes, yes, there are crafty work-arounds. Each with its own pros-and-cons. The point is that the IDE itself was designed to totally ignore the underlying file system. Let's put it this way: If I wrote code like that at the many jobs I've had over the years I would have gotten fired in a microsecond. Yet, for some reason, this is "feature" is now considered good design?
Back to coding.