The oh-so-quaint folder metaphor directly correlates to how humans do things in the physical world. I put my winter coat in a closet. My winter scarf, boots, hat and gloves are also in the closet, but in a box on a shelf.
My system may not be the same as yours, but it works for me. Dumping my winter stuff with all of my clothing on a pile, and affixing a blue tag on it to represent "winter stuff" isn't improving things. Installing a database-backed clothing management system like you would find at a dry cleaner in my house solves my organizational problem, but introduces alot of complexity and overhead.
Let's be real here. The reason that Apple is doing this is that have had success in delivering a dumbed-down API that makes their life much easier on phones, and prevents pesky third party software developers from doing dangerous things like allowing applications to talk to each other. They've decided to bring this innovation to the general purpose computer.