1. Gnome is at 3.6 they have many things that are changing rapidly. I don't expect them to limit the things they can do to make the DE _better_ just so that they have a stable API for themes.
2. I actually find myself liking gnome3 and gnome shell better then Xfce ( my fallback for the early days of gnome3 ).
The workflow they introduced hurt at first because it was different and scary, but its so natural now I find myself missing it when I work in Xfce or KDE. I know there are some developers who value above all else the freedom and ideals espoused by the FOSS movement and want a system stack that is true to those principles above all others. I am actually enjoying a well _designed_ and coherent desktop experience. Also I have the source code if something really is bothering me I can change it, but I am finding after 15+ years of tweaking config files to get everything to work the way I wanted it to I am now content to just have something that works out of the box even if I have to acclimate myself to some of its nuances. It turns out most of the time what I thought was a problem actually works better for me once I get used to it.
It's pretty easy to replace Nautilus with Nemo though (the Cinnamon fork version that emulates the old Nautilus).
The Gnome team would be wise to listen in on the feedback from the community. If they want a community that is. They seem to think that this "Gnome brand", "Gnome identity" and "Gnome platform" is the most important thing they need to concern themselves with these days.
Not being able to drop a shell script into some place to make GUI file management easier is a regression. (I say "some place" because when I was using this feature, it took forever to find the right place as it changed between released/distributions and I had to experiment to find the right set of env vars that are set, because docs were lacking).
Why don't I get to decide this for myself?
I've been using gnome 3.6 for the past month. I've been using Linux as my primary desktop for 18 years. I live in emacs. (unix cred established?) gnome 3.6 may not be perfect, but it works well. It's actually remarkable simple. I may go back to using awesomewm + gnome fallback, but gnome 3 is a solid desktop.
Guess what, not a good recipe for love of community.
There's a lot more uphill to go; it is actually quite nice to use as a day to day frontend already though.
Some of the things the api changes that have caused pain now will actually make things better over the longer term; take theming - it's all moving towards a CSS driven style.