1. It is an unacceptable UX to go "I wish I had feature X, but I don't, so lets go google search for a shell extension that provides it" then use the extension affiliation for Chrome / FF to install it. I got way too frustrated after looking for a way to make the super key not take over the whole screen (like Win7 / Unity don't)
2. There is a dire lack of a unsettings / Ubuntu Tweak style configuration editor for Gnome Shell. I don't want to read a book to figure out what my desktop can or can't do in the form of the shell manpages or help pages. I don't want to be forced into having the panel only show up in superkey mode, or to have to scrounge for a setting to enable that behavior, etc
3. I just plain don't like the usage of web technologies as a way to alter the desktop. In general, scripting languages inherently waste memory and cycles in favor of getting something done fast. But when you want a fast responsive desktop maybe the overhead of jaggermonkey (I think that is the JS backend they are using) is just insane.