I still think using Linux would be best. The other guys kinda wanna jump in head first with some of these ideas, like a single system folder, but I think taking it incrementally would be better... like building a new graphics framework.
X11 has been around forever and it's well documented and all, but it's also hopelessly outdated. We want to build a full Ghostscript or PDF-based desktop compositor that renders with OpenGL, much like Apple's Quartz Extreme does. Our working name for it is "NQ" for Not Quartz. Priority goes to video cards that are capable of running the GL-based renderer. Other cards will have to wait until a generic display-Ghostscript engine is built. But, since most machines today have cards that are capable of this (a notable exception is anything with a Rage128 series GPU. the R128 is incapable of textures that are not power-of-two sizes. 32, 64, 128, et cetera)
X11 compatibility will be implemented via a "classic mode". X11 apps would run alongside apps that use NQ but wouldn't be able to take advantage of any of NQ's advanced features.
The desktop will be built from WindowMaker and GWorkspace (the oss version of the NeXT Workspace manager). In the beginning, we'll simply use WM and GWorkspace as they are, and leave all the UI work until the end. We have no plans for what the desktop or the system's overall appearance will be like yet. If anybody is an interface designer, we'd love to have you on board. I've got a number of ideas to share on the subject, if you'd like to hear 'em.
As for the folder structure, it seems better to do it a little at a time, and start with this structure,
/private (this contains the typical UNIX folders like /bin and /var. there are invisible symlinks to these inside of /)
/Applications
/System/Library
/Library
~/Library
In the end, this is what we'd like to have, though
/Applications
/System
/Library
/private
~/Preferences
With NeXT/OS X, there is a private Library folder inside of ~/ which can contain DIFFERENT things from the System/Library folder and /Library. I think that, honestly, for most people, this can be improved.
By keeping only application-specific preference files and the like (mailbox files, browser caches, UI options, et cetera) inside ~/Preferences using XML files, the way NeXT and OS X do, all of that is separated fully from the OS. In the event of a failure if you have to reinstall, the whole OS is in /System and can be replaced rather easily.
/Applications contains the major applications used by the OS. MP3 Apps, and junk like that. Command line apps don't belong here. They go in /system/private/bin.
Legacy (Linux/X11) apps would also end up in their proper place inside /System/private/.
Apps built for this OS would be contained in .app packages. The binary, and all support files that are needed are inside the package. You'll never see anything ilke
/lib/libexorugal.lib.so not found
The higher-level parts of the OS and the apps will use APIs, frameworks, extentions and libraries that ride atop the UNIX layer, just like in NeXT/OS X. We're wanting much, much less of a UNIX clone, and much more of a high-performance desktop OS that's suitable for the masses.
As we go, we'll be able to look into other things, like integrating multimedia features, maybe using OggVorbis as the built-in audio/video codec.
As the project goes on, we'll also set out to make several consumer apps, in the vein of Apple's iApps. A movie maker, an audio library/player, and a photo app.
These are just a few thoughts... I hope we can generate some interest, get the project going, and have a real replacement for Windows before Longhorn arrives!