Autotools-based build infra is always crufty, fragile, slow, and fugly. In a lot of cases, it sucks because it's what we have right now without doing the work to replace it with something equally flexible.
Build infrastructure should be minimal, standardized, and not subject to endless special, undocumented fragility.
cmake, just, conan, meson, and bazel (and forks) exist.
But I've still yet to see a proper build system that does feature detection in parallel and concurrently, or supports live, incremental, continuous, cached rebuilding.