Basically what it came down to was a reader who worked for an OEM said that the real problem is that it's too expensive to produce software that works well with both manual and automatic transmissions if very few buyers opt for the manual transmission. In other words, its about the price of investment versus the derived benefit from that investment. Automakers aren't running charities (actually they all run charities, but that's another discussion for another day). They are in the market to make money, so they produce what they believe will be profitable.
The sad truth is manual transmissions are not dying outside of the United States. If you go car shopping in Europe you will find that many models can still be had with a manual transmission. Americans like a computer to do the shifting for them, despite issues like gear-seeking and a general lack of control. Sadly, I have to admit that right now I do not own a car with a manual transmission and have not for a while. Do I like that? No! If I had the extra cash right now I would buy something with a manual transmission just so I can feel the exhilaration of letting the RPMs climb before throwing the car in the next gear or of dumping it into a lower gear and feeling the car rocket forward.
And that's exactly what we as driving enthusiast Americans (if you are American, like me) need to do. We need to get out there and buy models with manual transmissions! If nobody buys them they will go away. You can get them on a number of vehicles still, so go find a vehicle that works for you and have at it. Now for me to figure out how to afford a new BRZ with a manual transmission so I can support the effort...