Manuals - any Manual transmission - can outlast the Automatics in many ways - as long as they are taken care of and not abused.
So service records and a good - independent - mechanic to inspect the vehicle can go a long way - for any type of transmission and/or engine - to help you negotiate a good price.
Manuals are not "a big selling point" but prove their worth when it comes to being in control of the vehicle and able to withstand what nature puts it thru,
Many times, people never had to replace a clutch in a manual because they learned how the engine rev sound - vibration and feel - work for them They become part of the vehicle and enjoy the effects and confidence of being able to control the vehicle in shifting and performance.
But the Automatics have speed and the automation that makes them "quicker" - but only to a specifc degree - they do have "lag" and the conversion of torque to acceleration - (Fluid transfer from one to another - torque converter operation) the manual seems to benefit from this.
I'd like to see Ford take more concern to the ratios - so the Manual and Automatics can be nearly equal in performance - might make an extra gear of two in the manual a requirement - but there are also other factors that come into play that Ford could utilize in their transmission designs - up to and including a gear ratio that allows the higher gears to offer more fuel economy when long commutes as high speed (read as above 45MPH) - traffic speeds can boost the fuel economy of any vehicle.
The "Ford Transmission Problems" you hear about have been with DCT and use a system of electronic clutch actuators to mimic an automatics' shifting and drive-feel. DCS is another type which is the "Sport" version.
Being from a CDL over - the - road (OTR) driver - a typical 5 speed transmission with a splitter gives you a very wide range of gears to choose torque to acceleration options and controls - I can attest the having a few extra gears does not hurt the driver. It's just the opposite, it can make them more effective drivers - they just need to put the phone down and drive