It's a matter of not just personal preference, but of usage.
If you like to drive like a race car driver (to the floor when it goes green, seeing how fast you can take a corner, seeing how fast you can go up a hill, determining your quarter mile from light to light, burning rubber) then you want an manual. It gives you a bit more control over the torque, power, slip, and acceleration than an automatic transmission.
Additionally, if you do a lot of towing (unlikely with a Mustang) or winter driving, you may prefer a manual transmission because it allows you to slowly down shift, using engine braking to slow your vehicle when road conditions (or trailers) prevent you from slowing quickly.
If you're using it as a daily driver, from home to work and maybe the grocery store, then you may prefer the automatic. It allows quick jaunts with less dedicated attention to the car itself. If other people will be driving your car at all, automatic may also be a consideration; less and less people know how to drive 'standard' transmission vehicles.
The final consideration is personal preference; what pleases you more? More comfort or more control? More involvement in driving or less? Torque or consistency?
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"I'm typing on a computer of science, which is being sent by science wires to a little science server where you can access it. I'm not typing on a computer of philosophy or religion or whatever other thing you think can be used to understand the universe because they're a poor substitute in the role of understanding the universe which exists independent from ourselves." - Willravel
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