That process didn't start with GNOME 3. GNOME 2 is a result of the exact same thing. And I'll enthusiastically disagree with your assessment that it was the "best desktop environment of its day." Maybe it was great if you were coming from Windows, but coming from earlier versions of GNOME or from other UNIX DEs, it was lackluster at best.
Sun provided UX people for GNOME because it wanted to ditch CDE (ironically, right after it had switched to it from OpenLook). The Sun people came in and said, "fuck the power users, let's make things easy!" Options were considered confusing and omitted. The traditional UNIX workflow was replaced with a very Windows-like workflow. This lives on today in MATE - if you compare the standard Windows workflow with MATE, it's basically the same.
Metacity is the perfect example here. It's the most brain-dead, unconfigurable window manager ever. It's less configurable than TWM. Thanks, GNOME, no, I don't want to be productive, what a silly idea! The first official WM for GNOME was Enlightenment, which was all kinds of configurable, and then Saw[mill|fish] (which I've been told was very configurable, although I didn't know LISP at the time so I never found out for myself). Going to Metacity was pretty much par for the course and indicative of their "options are evil" mentality.
Those of us who started using GNOME back in the 0.x days watched our beloved features go away. Some adapted. Some, like me, ditched GNOME as a DE and ran a mixture of various software, including GNOME and KDE apps, and put up with the times when stuff just didn't work right. I eventually switched to KDE, since KDM can do most of what I wanted FVWM for and supports something closer to the traditional UNIX desktop workflow, but I can see where the UX people have been "innovating" there too.