I know this is an old question, but I believe I can offer a few insights.
You’re correct: content-centric is more akin to how humans think. Using tools is in our genes, but apps are not tools: they’re silos of tools.
In the real world, we have tools like a paintbrush; in the digital word, we also have tools like a paintbrush. In the real world, you can take your paintbrush out of your studio and use it anywhere you want. In the digital world, the paintbrush tool is stuck inside whichever app you’re using. If you want to use it in some other app, you better pray the app has a similar tool.
If our operating systems were designed around content instead of apps, the humans using them would never have to think about apps. Instead, you’d have the stuff you care about (the content), and you’d manipulate it with tools that you could use anywhere, on any document. Then our digital world would match how our human brains evolved to work in the real world.
So, why don’t computers work this way?
The first graphical operating systems were document-centric: Douglas Engelbart’s NLS, Xerox PARC’s Alto/Star, and Apple’s Lisa. None of them exposed the concept of a program or application to the user. Instead, users worked with documents, and the computer handled how to display and modify them.
I believe the first operating system that exposed the concept of an app to users was Apple’s Maacintosh. I don’t know why such a change was made. I can only speculate. I suspect it was easier to program. Perhaps Steve Jobs imagined a thriving market of applications for his new platform. No matter what the reason, we’ve been forcing humans to deal with this new concept ever since, for better or worse.
Having to manage both documents and applications—two separate and very different paradigms—can get confusing for ordinary people. So, to make things “easier”, operating systems started to emphasize apps over documents. Now, people only have to manage apps, leaving document-management to be reimplemented by every single app. This started with mobile devices, such as Palm and the iPhone, but now desktops are imitating this way of thinking as well.
People have forgotten about files. Their stuff lives inside apps, and they have no idea how to get it out of there. Want to organize everything related to a single project all together? Your computer won’t help you. It may not even be technically possible, depending on the apps that you use.
Experts have been making these points since the beginning. Jef Raskin (the father of the Macintosh—until Steve Jobs took over the project), wrote about it in the Humane Interface. His son, Aza Raskin, gave a talk about it. And even Edward Tufte made this point:
Interfaces have been made inconvenient by computer companies selling applications and operating systems; their economic needs play out on our interface, by giving us apps and operating systems instead of documents.