There are a couple of reasons why your horse may have a short, choppy stride. Oftentimes, horses with a steep shoulder and pasterns have short, choppy strides. Evaluate your horse’s conformation to see if this may be causing this type of movement. Remember that the angle of a horse’s shoulder and pasterns should be 45 degrees. If your horse is more upright (steep) than that, it is likely to cause short, choppy movement. Also, check his hoof growth. Have a reputable farrier evaluate his hoof conformation to see if any changes need to be made.
If neither of these scenarios fits your horse, make sure you are riding with your seat and legs to ride your horse from back to front into the bridle. Horses that do not engage their hind end often lack the suspension and self-carriage necessary to lift their shoulder and extend their stride. You might consider working with a reputable trainer on these skills.