I have to ask whether you've ever used Microsoft's OS. The interface varies from tool to tool and many applications completely ignore all standard UI guidelines. Windows Media Player continues to eschew all expected interface decisions. Even Microsoft Office 2000 was different between Word and Excel (MDI versus SDI). I agree that more commonality between all applications and OS components helps, but it clearly isn't a hinderance to "user friendly" status.
Sure, if the average user decides he likes Gnome best, he can still use KDE applications, but the little inconsitencies in the interface will start to wear on him. Why is that? Because the inconsistencies lead to things not "just working". Users don't want to have to know 3 different ways to paste something based on what toolkit the app is based on. They just want to go to Edit -> Paste (the more savvy ones may know Control+V) and have it work.