Sorry for bumping an old topic, but I recently found this nice template and used it for my MEGA shield design.
Firstly, thanks for the effort, friend! I really like the 3D
It appears that the digital header is wrong. It is mirrored (or something like that). For example, IO23 pin is sitting next to the label of 22. This can be fixed easily by double clicking the hole and changing the NET.
Too bad I didn't catch this before submitting my PCB! Not a huge deal, though, since I can take care of it in software.
Improvements that can be made to the template:
Fix the digital header
Add a cutout around the USB connector
Increase hole size to 40mil from 30mil for the headers