In regards to shadow reduction or image touch-ups, you can batch process all shots before running them through your photo stitching program using Lightroom as @David_Brooks mentioned. I've done this on a number of projects with great success. Another photo editing program called Photo Studio from ACDSee will help with batch processing as well, but at a lower cost than Adobe. For the past month I've been testing the ACDSee program's Light EQ tool and using settings other drone mappers have been using and I'm impressed with the results!
Of course the images should be fairly dialed-in through the camera settings for each flight, but out in the field and flying numerous jobs in a different location on a single day, nothing is perfect.
If folks are interested, I can post those ACDSee Light EQ settings.