I'd say on some platforms "horrifically slow" is an understatement. At my day job we were building software in Cygwin on Windows machines infected with Symantec's virus scanner which adds hundreds of milliseconds to every process launch. The configure script for Protocol Buffers took something like half an hour to run.
We eventually switched to CMake but not without a lot of pain first. For what it's worth, CMake fixes the speed issue but not much else. It still has its own totally esoteric custom language, it still discourages globbing source files and requires re-running upon adding any file or changing anything, and it has even more insane default settings than autotools (for example file(DOWNLOAD) from an https:// URL by default ignores certificates!)
There is something wrong with all of these buildsystems. I don't know what the solution is but I feel we are very far from it.