It has been this way for years. Manufacturers usually only offer the manual transmission with the base package or the enthusiast option. Few people want the base package. Not as many can afford the enthusiast option. A number of people who would prefer a manual settle for an automatic to get...
The keypad is one of my favorite Ford features. I use it on my pickup frequently. I've actually chosen Ford products over good competitors just because of it. I plan on getting that option.
Antimatter Blue is how I voted, but may decide to go with black. Most of my cars have been black, but I prefer a metallic black because I think it helps hide swirl marks.
As far as the manual transmission, manufacturers seem to only be pairing them with the least powerful engine choices these days. Then, they say few buyers order them. That shouldn't be a surprise, but apparently it is. I would love to have a 2.7L with stick shift, but doubt it will ever happen...