Earlier quoted context omitted.
I don't know if it ever was a "kernel up" development process. Gnome (and KDE) both had their own, pretty complex stack, even before Freedesktop.org came up (e.g. KDE had DCOP and a bunch of other services). And they weren't exactly bug-free, either -- but at least they covered a lot less surface. I don't think it's a simple problem, and I don't think all the blame should be laid on Freedesktop.org, where a lot of go…
Not in a planned sense. But until Freedesktop, i had the impression that you had the kernel, then CLI user space, and the X and the DEs that wrapped the CLI tools in certain ways and the CLI tools in turn talked to the kernel. Thus you could go from bare kernel, to CLI to GUI in a layered manner (and fall back when a higher layer had issues). With Dbus etc the CLI has been sidelined. Now you have a bunch of daemons t…
Unfortunately, there is a lot of weird interaction between all these processes. It's often badly (or not at all) documented, and what plugs where is extremely unclear. It's very messy, and it doesn't stand still long enough for someone to fix it. They just pile half-done stuff over more half-done stuff.
It's really unfortunate because the Linux kernel is, pragmatically, probably the best there is. It may not excel in specific niches (e.g. security), but overall, it does a lot of things better than, or at least about as well as BSDs, on systems where not even NetBSD boots.