I'm not saying everything has to have a software solution, but there is a lot of flexibility that software can provide. And when the government starts mandating fuel economy numbers or a penalty if those numbers are not met, manufacturers have to get creative with weight savings and efficiency. A low current wire or two and rotary encoder dial with some software weighs a whole lot less than a mechanical linkage, or even a sturdy large lever intended to mimic a mechanical gear selector. Plus, as mentioned before, it has the added benefit of being able to implement safety features not even imaginable with the old mechanical method.
Additionally, there's no way fuel economy and emissions of an internal combustion engine would be anywhere near where they are today without the incorporation of software.
While I'm not a software engineer or a gamer, I can certainly understand there are several benefits to incorporating it into modern vehicles.
-Rod