Embed Camera calibration in the work flow:
As a start, allow one to specify the location of a camera calibration file and, if present, undistort the images prior to beginning other steps.
A tool to extract the camera calibration. It could be from images of a checkerboard pattern, or even a method like the one proposed at this link which describes (at a high level) a strategy for automatically extracting the calibration.
Finally, I second the wishes of others to improve the GCP interface. In addition to making it easier to find/match GCPs, there should be an interface to specify known lengths/heights of objects in the scene.