My first point on this is, as said by people on some of your comments, Alex is already working on gvfs, the Gnome VFS replacement, and his work looks promising, and the most important, it's usable already.
The second point is, FUSE is not an option, GNOME is a cross platform development platform, or at least, it tries to be as cross platform as possible. Initiatives like GMAE, are based on that fact, GNOME should be everywhere.
FUSE is now working on Linux, yes, but it's far from being API stable (ask FUSE modules maintainers about that issue). It's not ported to as much systems, just FreeBSD and port in progress for OpenBSD (there are some people working on porting them to other projects, but we cannot make decisions based on that).
Portability is a big value for GNOME, and we shouldn't focus on Linux only. Right now, the POSIX marriage of GNOME-VFS is what kept some projects out to use it since they want their apps to work on as much systems as possible (see inkscape, gimp). A portable VFS is what we need, if we loose portability, we loose the chance to be the platform of choice for people out there.
Another problem is, FUSE is on the user space, that means, that for every I/O operation, there is a context switch, which burns out your laptop/mobile battery. Do we want a VFS layer that would be unusable on GMAE friendly devices? Again, choosing FUSE, make GNOME a less appealing choice.
Does this means that we should forget FUSE? Nope. I don't know if Alex has plans on this, but it would be great if gvfs could take advantage of fuse modules in a transparent fashion, so we can reuse existing code (which is the good point of your post Lennart), but I think that we should encourage the writing of portable plugins for WebDAV, SSH, Tar, Bzip2... etc. So I can write my app once and run it everywhere.