GNUstep-make now supports arbitrary(-ish) filesystem layouts. While the default is still the /usr/GNUstep layout with the various domains, one of the bundled alternatives is to put everything in FHS-compliant locations. Once that hits a release (which I believe will be called gnustep-make 2.0), that should make newbie users and distributors much more comfortable with GNUstep. I also provided a NeXT-ish layout which doesn't clone the NeXT directory hierarchy, but rather mimics it sensitively.
My work laptop just earned itself a reinstall (I'd been uncomfortable with CentOS for a while, but the facts that hotplug isn't configured properly and every time I 'yum update' I have to fix a handful of drivers drove me over the edge), so when I re-create my GNUstep installation I'll do it with the new-style make. I'm currently wavering on the side of installing Midnight BSD, but I might wimp out and dual-boot Ubuntu ;-)