It's not just about security. It's also not just about CPU architectures. Most people assume the ARM vs x86 issue is the biggest problem, when that's not even half of it.
Far more important is the fact that none of the desktop software developed for Windows, nor even the Windows OS itself, is suited to running on ultra mobile (resource restricted) devices like smartphones. There are a whole host of problems this causes, most of which are basically unsolvable. It's was obvious that Win32 could not retain compatibility with existing software, while also providing a runtime environment that is well suited to low-power devices. That was basically the starting point for developing WinRT (API and runtime).
I'm sure we'll soon have the technology to carry around a desktop OS in our pocket, but the bigger question is if we'll ever want to, considering how much better such devices are when being restricted to running only low-power optimized OSes and apps.