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Depending on the company, these costs can vary quite dramatically ...

In the past some CPUs, GPUs and other components have been designed (more or less) from the ground up for a company and the development of these components can often cost hundreds of millions or billions of dollars without including technology licensing fees.

Nintendo has been known to outright buy the design of a particular component to lower per-unit manufacturing costs and to give them the option to take it to another manufacturer to produce the component; with the XBox, Microsoft didn't do this and when nVidia refused to continue developing the GPU Microsoft had to stop production of the XBox.

With something like controllers you might assume the R&D costs would be low, but for each controller there are (probably) multiple tech-demos created to prove its value; and there are probably a lot of "failed" controllers produced for each successful one. I could be wrong but I wouldn't be surprised if Nintendo had multiple HCI teams working constantly on projects, with each of these teams having a budget of (something like) $5 Million per year, to be able to produce a system and its accessories; often with a lot of "failed" concepts because they're ahead of their time, too expensive, or not accessable enough. Over a 6 year period these costs add up dramatically.