Minecraft has a somewhat complicated development history. There are multiple versions of the block-building zombie fighting game developed in parallel. The original Minecraft, built for PCs and with a rich ecosystem of third-party extensions, is a Java application. Console versions of Minecraft appear to use a C++ port of the Java version, with a console controller-friendly interface. Minecraft Pocket Edition is a C++ application with a user interface that's tailored for smartphones. Multiplayer is generally limited to the same stream of development; Pocket Edition players on different platforms can play with each other, but Java edition players can only play with other Java edition players, and the console editions only allow multiplayer with other people on the same console.
The Windows Phone/Windows Mobile version of Minecraft was Pocket Edition, and this version remains supported on Android and iOS. Pocket Edition is also the basis for versions of Amazon's Fire OS and Fire TV, Samsung's Gear VR, and the Apple TV. Pocket Edition is still relatively new: after a lengthy alpha/beta period, it only hit version 1.0 on December 19, 2016. Although Microsoft released multiple beta versions for Windows Phone, including the final beta version 0.16.2 on November 18, 2016, the platform hasn't had a version 1.0 release. It's stuck on the final beta.
The company has, however, released version 1.0 of Minecraft for Windows 10. Minecraft for Windows 10 is based on Pocket Edition, but with a desktop user interface. It's built for Microsoft's Universal Windows Platform (UWP) and sold exclusively through the Windows Store, but as it's still based on Pocket Edition, it supports multiplayer with the smartphone versions.
This makes the situation look rather awkward for Microsoft. Since the release of Windows 8, Microsoft has been encouraging third-party developers to build applications for UWP (and its Windows 8-era precursor, WinRT). The "universal" part of UWP is that UWP applications can run on desktop Windows, Windows Mobile, Xbox One, HoloLens, and even the Surface Hub. The goal of UWP is for the majority of an application's code to be common across all form factors, with a user interface tailored to each specific type of device.
But while this approach of having one application that spans multiple form factors is still the officially preferred route for third-party developers—and, to be fair, a good amount of first-party development; built-in Windows applications like Mail, Maps, and Calendar, as well as separate apps like Office Mobile, are all UWP apps that run on both mobile and desktop systems—it's not the route that the company has elected to follow for Minecraft. Minecraft for Windows 10 is a UWP app, but rather than give that UWP app an adaptive user interface that works equally well on all UWP platforms, Microsoft has kept it strictly desktop-only. It won't run on Windows 10 Mobile.
Update: a previous version of this article said that the Phone app was also a UWP app, but of course it cannot be, as it runs on Windows Phone 8.1. C++ app development on Windows Phone 8.1 has a lot of overlap with WinRT and UWP, but the platforms are not identical.
Eventually, one imagines that Microsoft will bring back support for its mobile platform. Windows 10 Mobile and Windows 10 development is continuing to converge—Windows 10 for ARM may well end up on phone-like devices and larger systems—and Minecraft for Windows 10 will start supporting more form factors, with Microsoft promising a HoloLens version of the game. As Windows narrows and Minecraft for Windows 10 becomes broader, one can imagine that a mobile interface will be added to the Windows 10 version.
In the meantime, however, the game stands as yet another anomaly in the company's approach to software development. It isn't following the rules it suggests that others should obey, and third-party platforms—including the relatively rarely used Fire OS—are seeing stronger software support than the company's own. This tendency to offer better support for non-Windows systems continues to annoy Windows fans, and the failure to capitalize on the universal-ness of UWP leads developers to wonder, "If Microsoft isn't consistently writing universal apps, why should we?"
That's still a difficult question for the company to answer.