My computer is my computer. Not Apple's computer when I'm using iTunes (hah, as if I'd ever use that piece of crap, but stay with me here), not Microsoft's when I'm using Windows Media Player, not Google's when I'm using Chrome and not Mozilla's when I'm using Thunderbird.
I know what I want my user interface to look like. I know what fonts, colours and relative sizes I want things to be. All in exactly the same way that I know what colour I want the walls to be painted in my home and where I want my furniture.
By breaking UI conventions because some idiot thinks that he knows what colours and shapes my monitor should display, I am unable to dictate what my own things should look like. Instead of a designer spending his time on designing a theme for a GUI toolkit and skinning all of the applications on my computer at once, he wastes time on coming up with a visual theme for just one of them.
Intelligence 101 - tend towards abstraction as much as possible. This recent trend clearly has it's roots in the idiot depart... ahem, sorry, I mean marketing department where the thinking went something like "but we need to solidify our brand experience by making our application stand out!". Yeah, buddy, yours and everybody elses. Give me my shit back, provide the functionality I'm buying from you and design a nice theme for KDE or Windows if you feel so inclined.
To hammer the point in further with another example, CSS was designed with, err, designers in mind and look at what a head-fuck that turned out to be. Leave the thinking to people who know how to think - we'll tell you what needs prettying up and how to do it right.
To throw out an idea of how things could be better - why can't GUI toolkits support fluid designs which can be manipulated by central themes? Why can't some people opt for ribbon menus while others use the old drop down menus just by changing a theme? What about if I want all my menus to be ribbon style but in a vertical fashion? Or if I want that list of porn actresses names' to be on the right rather than on the left of the porn database application I use to track my stalking habits? GUI's should adapt to how the individual thinks as opposed to the other way round as it currently is. That is the smart way to do it. This recent trend in UI's and, frankly, many other things, is taking the stupid approach to the problem.