The newer XBox consoles are x86 architecture devices with an operating system that is similar to Windows. If they can maintain retrocompatibility with older titles, that means they have a functioning emulator or compatibility layer for classic XBox and 360 games. It would be trivial for Microsoft to release them for PC but they don't seem interested in doing that. Whatever obstacles there may be there, they are not technical. Considering that, it's unlikely that they would take a different approach regarding older Nintendo titles.
The example of Age of Empires II if anything indicates that they want to have a console-centric approach towards older titles. So, it's just speculation to assume that Microsoft acquiring Nintendo would lead to their games being ported to PC. On the flipside, I'd be more concerned that Microsoft's more inconsistent quality standards and monetization tendencies would make their way into Nintendo titles.