They were too early, and then too late. CE and Mobile just never had devices with enough processing power or good enough hardware UI to make them viable and enticing for developers.
In retrospect, after understanding more about tech history, I suspect the leadership of Steve Ballmer during the vital period in the late 2000s and Bill Gates' spending less time on Microsoft probably had something to do with this as well.
According to reported stories, Bill used to be really good at understanding how to squeeze the last drop of performance from slow hardware, a vital skill to have in the 1980s, yet subsequently became less important when desktops became fast enough. If they had Bill Gates leading the technical direction of the mobile OSes, the extra focus on speed optimization might have been what would have allowed Microsoft to do better during the smartphone wars.