Affine fits a different X and Y scale. Software written without professional expertise. Least Squares gives great weight to outliers, so residuals can be misleading. Redividing the Labor Robust Statistics can tolerate blunders. Models such as LMS offer a redefinition of error.
Research community can innovate.
Innovations should be launched into practice. GIS users should expect better registration, but don't know to ask. Software vendors should change. Persuasion requires a comprehensive approach to socio-technical networks. Innovative ideas should alter practices.