Here is my pipeline how I process GoPro video footage after flight. I have found that it is necessary to handle video footage before import in it to editing program. I use After Effects CC to make all important preprocessing steps. Warp Stabilitzer VFX is the most valuable effect which will polish video shots and make them smooth. With Optic Compensation I remove the fish eye lens distortion which is quite strong in GoPro picture.
After these steps I import the rendered footage to Final cut pro X and start real editing.