A lot of large projects* I use were formally autotools, and now use CMake. CMake is by far easier to maintain and allows easier integration this code in other projects with dependencies. I will agree that the documentation isn't great, the only way I was able to use it meaningfully by understanding how larger established projects utilize it.
http://www-public.slac.stanford.edu/geant4/
https://root.cern.ch/drupal/
https://www.kde.org/