Just because you have a Mac doesn't mean you have to use iPhoto, just like you don't have to use Windows Live Photo Gallery if your OS is Windows 7. Use Aperture, Lightroom, Picasa, ....
For me, the advantages I get by having iTunes or iPhoto manage my libraries with metadata far outweigh having to do everything myself in the file system. It's very hard to get an equivalent of Smart Playslists or Smart Albums when trying to organize things in the file system.
Just a couple of points for your example.
- The photo "archive" is a bundle. i.e. it is simply a directory. "Show File" in iPhoto will take you right to the location of the picture in iPhoto. If you know the name of the album it is easy enough to find it without opening iPhoto. Show package contents to "unbundle" the iPhoto library.
- If you edit or modify within iPhoto (which most users will do at least for most simple operations) creating the copy is done for you.
- Drag and drop. Drag from iPhoto to the file system, edit, drag it back. It's really not that bad.
I think the success of the iPad and other iOS devices shows that an exposed file system is not the only way to go and that not having a filesystem at all can work for many types of task.
Microsoft recognized this and promised us WinFS, but so far hasn't delivered on it, while Apple has given us iTunes for music, video, books and iPhoto for photos and video.
That said, I always hedge my bets. While iPhoto is my main tool, I also keep a separate file system directory tree library with the raw photos as taken from the camera or scanner (and another for edits) on my NAS. This way if I choose a different OS or photo organization tool I can start fresh quite easily.
B