After a quick glance at a few system spec requirements for the commercial game Prototype (thank you Google), it looks like Prototype requires and uses DirectX, and is available for Microsoft-based Windows PCs and X-Box. I'm guessing that the software was built and compiled with Microsoft libraries/compilers/programming tools and such.
I'm not an expert programmer yet, but I'll do my best to explain this as best I can from what I've gathered over the years (Mattn correct me if I'm wrong on any of these points):
Many "off-the-shelf" PCs from stores are built and rigged for such commercial software, but in my experience not for GNU-based free software or open-source programs like UFO: AI. The Windows port of UFO: AI is built with MinGW, which is a very different beast than any Microsoft compiler.
IIRC DirectX is a "Microsoft-thing" while OpenGL isn't, but is an open standard.
That doesn't mean that you can't run stuff built with MinGW or open standards on new computers efficiently, it simply means you need drivers that support such software.
Windows Update does *not* typically provide drivers with such support. Fortunately, some hardware manufacturers provide drivers that do support things like OpenGL and such.
This means, as an example, that if you have an NVIDIA video card and want to run an OpenGL-based program, you should not update the driver with Windows Update, but instead download a new driver from NVIDIA's website, directly.