Windows IoT Core's main target is education and hobbyist users. It does have a GUI stack but is limited to Microsoft's Universal App Platform (UAP), which is not a bad thing if you are interested in developing C# applications using XAML or HTML.
You are not strictly limited to the previously mentioned technologies. Microsoft tries to support a few other programming languages, such as C++ and Python with UAP SDK, but also native Win32 applications or services with some limitations.
The other benefit of developing universal apps is that you can install them on any device running Windows 10, even a full desktop. So, it is easy to distribute one code base to the Raspberry Pi 2, Intel Galileo, or MinnowBoard for embedded applications. Also, for remote managing console to your Windows 10 Phone, Tablet, Desktop, or Xbox.
Windows IoT comes with a lot of criticism from the Linux community as to why Microsoft even bothered doing all of this. Essentially, the point is not...