A lot would depend upon your location, meaning your altitude and flight speed. Night time or day time? I would want to stop down my aperture to f/5.6 to f/8, in order to take depth of field concerns out of the picture.
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I would go with a wide lens over a long lens. With a wide angle, you pre-focus at infinity, and everything would fall into focus beyond a few dozen feet. A full frame camera's wider angle of view would be an advantage over an APS-C camera.
With long focal lengths, not only does focusing becomes a worry, air speed becomes with longer and longer lenses. At most flight speeds, the ground is racing past you at fairly high speed. Your images could become blurry at telephoto focal lengths.
Finallly, I would manually select just the center AF point. But, as I previously noted, if you use a wide angle lens focused at infinity, you could turn off AF on your lens and simply shoot away. Besides, the camera may have difficulty focusing because it might hard under the circumstances to aim at one object long enough to lock focus properly.
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