As electric and hybrid cars take over the product stacks of the manufacturers (for example, Ford aims to have a hybrid or full electric vehicle in every market segment they serve by 2022), manual transmissions will become harder and harder to find (electric cars don't have a "transmission" in the traditional sense and there are no manual transmission hybrids on the market).
The fuel consumption argument is also disappearing due to automatic gearboxes becoming more intelligent. And in my experience, drivers of manual cars tend to drive more aggressively, which would more than compensate for the 5% difference in consumption that you estimated.