It mainly boils down to two essential points: flexibility and arrogance. GNOME has been "simplified" more and more for some time now, almost always at the expense of flexibility and configurability. And when someone complains, the reactions often are along the lines of "we know better than you, we will not change it back, so get used to it or get lost". Want examples? Sure.
1) I use a focus scheme usually known as "focus on mouse contact", and am used to being able to trigger mouse events in a window (i.e., 'click') _without_ raising it. While Metacity fortunately still can do this (so the wm itself is not to blame here), why on earth do I have to set this in a lousy 'regedit' rip-off (which of all things pops up a window telling me I am not supposed to use it anyway)?
How is a tree-node GUI interface to a complicated XML file a "regedit" ripoff? There's quite a few configuration values stored in gconf that no-one wants to see - like x y coords for window placement or window size values. How do you propose to decide which options are in the "front-end" configuration and which are in gconf, or what would be a better interface to gconf? I'm sure there's a better interface to gconf, but it looks basically like an XML editor.
2) I am used to and can productively work with browse-mode file managers like Nautilus used to be until GNOME 2.4. In GNOME 2.6 spatial mode was added. Fair enough. But why does the upgrade simply change the default behaviour without asking me, seemingly expecting me to re-learn before I can get any work done? That is quite arrogant. Again: the possibility to switch off spatial mode was first hidden in the GNOME configuration editor and only added into the GUI of 2.8 (AFAIK). And yes, I have tried spatial mode, albeit not for very long. Desktop environments should help me improve my productivity, not force me to re-learn all the time.
It probably would have been better to have the GUI config for "browse by default" in 2.6, rather than waiting till 2.8. That said, I don't think a one time move to spacial navigation constitutes "force me to re-learn all the time".
4) Simple details of themes, like the size of icons in applications cannot be modified. The icon size and arrangement of most themes is almost ridiculous. At least on a 1024x768 laptop screen. Simple possibility to reduze size and space between icons? Not that I know of.
This is somewhat configurable in .gtk2rc, iirc
5) Every directory having its own view settings in Nautilus is nice, but absolute nonsense without a "set this view for all" function. If it does exist, I did not find it. And manually changing the settings for every directory I ever visited is quite tedious.
In the file-management capplet the top option is "View new folders with:" and a dropdown.
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