mnm - enjoy your car. I like the way that my 2012 Focus SE HB with a MT drives. I am also glad that it doesn't have a turbo.
But, I am an outlier. I have purchased a 1977 Mercury Monarch with a MT (1st to second shift sends the stick back practically to the back seat), a 1974 Capri with a MT, a Ford Fiesta with a MT, numerous Mustang MTs, and of course, the Aerostar MT. Kelly Blue Book predicts private sales on my 2012 Focus (non-dealer) $6-8K with an AT and slightly less (but close) for the MT (only 50K mileage). The sales from a dealer are close, but slightly less. You are correct. If the AT didn't have a problem, the resale of the MT would be a lot less. Still Ford produced only 3% with MT on regular Focus, I think. The new Bronco has a 7-speed MT option on the lower series. I was surprised to see that.