I'm not sure about the Windows scene, since I only toyed around with one or two shells nearly twenty years ago, but the motivations for creating windows managers in Unix varied. Quite often they were about the appearance, customization, ease of customization, lack of customization, or low resource usage. I suspect that most of them were made for the learning experience or simply as a form of self-expression. They were never really about innovation. When there was innovation, it was usually in the form of small things like how we size and position windows (e.g. think about how it is possible to tile windows in Windows these days).

Besides, the term innovation is used far too much with respect to software, in the sense that a lot of stuff can be traced back much further than the so-called innovators will suggest. Many ideas have deep roots, but it took several (often independent) attempts until the technology or its users were ready for it.