What I'm really referring to is the ability to organise your music, photos, videos, and documents (all of which are files) in a way that is based on topic/project, not application. For content consumption I think the current approach is fine, but for content creation it's often necessary to deal with multiple types of documents (e.g. a spreadsheet, word document, and some photos) and it's really awkward to deal with this in the current model.
If you are working on multiple projects, you want all the stuff for project A in one place, and all the stuff for project B in another place. This is especially important when A and B are for different clients, or you want to collaborate with someone on B but not on A, and easily send others a copy of everything relating to B.
I've seen first-hand how novice users can sometimes get confused about the location of their files, e.g. my documents vs. desktop vs. whatever, and I definitely agree that we need a better approach than currently provided on desktop OSs. But I think iOS goes too far in the other direction, and we're still yet to see a solution that scales well with user skill level and needs.
mkay. I think the market disagrees with you a bit. And your strawman about being the "main machine" is contrary to Apple's goals. They would like nothing better than to sell you an iPhone, iPad and MacBook.