If I'm remembering right, Shuttleworth decided to go his own way because at the time Gnome Shell looked radically different than it does now, and he didn't forsee it--or the political environment around it--improving enough to bother building upon. However since he made that decision and showed some Unity prototypes, the Gnome Shell design did change a lot and now it resembles Unity much more than it did back then.
Yeah, Canonical wanted to participate in Gnome3, but nobody listened to their complaints about Gnome3.
I agree, Canonical should have made Unity upon gnome 3.x. Those compiz patches and are really nasty.
Compiz also seems to be in trouble:
http://smspillaz.wordpress.com/2011/12/25/apology-2/
edit: Yes, also https://extensions.gnome.org/ is pretty neat.