Are the alternatives worse, or are they just different? Obviously anything sufficiently different enough to be called disruptive is going to throw off your workflow. The mitigating factor in how much anyone is going to like change is how quickly they can adapt to the change. If the answer is never (or a long time), the change stops being relevant (think Dvorak keyboard). If the answer is reasonably quickly, you find a sliding scale of market penetration between trackball mice and computers that print stdout to screens instead of paper.
The question is, is the desktop metaphor still a good one? I would argue it never was good, just necessary. My question is, why do I have to move my mouse here and there to get things done on a desktop? Why is it so painful to use a laptop trackpad to get here and there with any accuracy? Newer window managers try to mitigate that by removing the need for a mouse altogether. That's a step in the right direction, I think.
Don't take my word for it, this is a falsifiable statement. Run usability studies on both novice and experience users with different desktop models and metaphors.
Ensure that you're not just testing initial impressions, but usability after a week, a month, a quarter, a year.
I've used Windows, Macs, and multiple Linux desktops for years on end. Hands down the environment that lets me get the most done with the minimum of hassle and interference is Linux.
My desktop (used on both traditional PCs and laptops) minimizes mousing actions by maximizing keyboard inputs to perform work and manage my GUI).
My favorite DE/WM is one where I don't have to click on a shortcut to launch an application. So in Gnome 2... well you can install Gnome-Do, but out of the box that fails. Gnome 3/Unity, just hit Super and type. Done. Windows Vista/7, hit Windows and type. Done. OSX has a similar feature from what I hear. There really is nothing more I need from a WM, everything else is value-add. The entire purpose of a desktop is to get me between applications.
I sure hope so. It's ideal for laptops and desktop PCs, or at least none of the alternatives are good enough.