The difference between long and short panels is the size of the raised square or rectangle part of the panel. On a 16 ft. wide garage door panel there will be either eight small squares along the panel and this is called a short panel. If it has 4 long rectangles across the panel than it is a long panel garage door. There is no difference in the doors cost or construction between long and short panels. The differences are strictly cosmetic and are only personal preference.
Short panel garage door
A short panel garage door will look a bit busier than a long panel door because it has twice as many raised squares on the door but other than that you will have to make the final decision.
Flush panel door
Some manufactures male what they call a flush panel door where there aren’t any raised squares and is just a smooth panel. These doors in my own opinion look better on a modern style streamline home than a traditional colonial style home. Be sure to make it clear when you are installing a new door which you will prefer or the door company will just assume you want a short panel door.