Overall, when things go wrong debugging cmake requires cmake knowledge, while autotools mostly require shell knowledge which is much more common (again, for sysadmins/packagers).
It's not really true because of CMake scripts much easier than tons of crap bash (configure) and m4 scripts in Autotools, also please don't forget Windows MSVC, Xcode and etc usage.
PS: I personally like Google's internal version of https://bazel.build/ a lot. I've never used open-source version but I presume it's similar. While it has many problems (Java, lack of popular IDE support, lack of popularity and, again, Java) good parts are rules are both machine- and human- readable and writable and generally easy to debug. I'm not bold enough to propose PostgreSQL to use it, but I'd be happy to see ideas from it to be used elsewhere.
We have many build systems, for example, another one http://mesonbuild.com/ but CMake the best today as meta build system.
