The reason most of your pictures aren't being used during the stitching process is due to the relative altitude in your area of interest based on the tallest feature. I would recommend increasing your altitude to around 350-400 ft and increasing your overlap to around 75-85 on both front and sidelap.
Trees are very difficult to stitch based on their complexity. By increasing your altitude and overlap you will gain more data and increase the common tie points between overlapping images. Here is a great document on flying agriculture late in the season that touches on many of the issues you might see while trying to map trees.