Perhaps you don't realize the amount of work it represents to build a consistent and solid user experience while officially supporting letting the user choose where to place its notifications, toolbars, etc, and never break this customizability afterwards.
I know, I know, I'm somehow objectively wrong for wanting this, which is fine if that's what you want to think. Like many others I left for XFCE a long time ago.
--edit-- fixed typo
The bad thing about it is the attitude, that users are being told they're wrong (constantly) and that the comparatively well-loved GNOME 2 was effectively declared dead and deprecated from day 1, instead of being respectfully handed off to the community or a maintenance team. Hell, G3 almost ought to have been called something else, and run separately. It's not the same thing.
And for the javascript customisation - some of the comments in the linked article seem to hint that the GNOME guys would like to ditch that too. It undermines the consistency of look and feel they're trying to achieve.
You should always provide a great default solution and let the user customize it if he wants to. Once there is ANY user customization, the entire user experience changes. If you want the UX to be ALWAYS the same, you can't let people change stuff.
The problem is, this is contrary to everything done before. I for instance, use Growl on OSX and customized it to my needs. The UX is the best one for me! It's not because Growl devs predicted that. They just let me CHOOSE after providing a great UX already by default.
Me, I like system notification areas that apps other than two or three 'official' gnome apps can use. I like to put my toolbars and menus in the place I want to have them. I don't know why you would consider this 'relentless customisation'.
Gnome hasn't sold out or gone mainstream, quite the opposite - they are losing people in droves, chasing some dream of going mainstream but actually slowly sinking into obscurity.