I honestly don't have any experience working with a team that produces a top-shelf title, like a popular web browser, spreadsheet, or calendar application. I've only been involved working on internal facing "intranet" business applications, because that's where the majority of the jobs are.
That being said, I wonder if what you're describing is worse for internal applications, simply because teams don't really "listen" to their users (employees)? I don't think I've ever seen a nice intranet or internal payroll application, for example. My current company, which is a very big F500 company, has one of the worst payroll and HR apps considering its size. Intranet applications tend to accumulate every departments special hidden feature without anyone keeping it in check.
Looking at Apple I feel that most of their customer facing applications and operating systems are getting worse not better. They are getting too "clever" with their user interfaces, relying on tricky unintuitive user interface gestures and hidden button clicking. I wonder if the symptoms you describe manifest themselves at Apple as UI "cleverness."