I hate using autotools, but every time I touch a project that uses something else (and that is too complex for a ten-line Makefile), I inevitably end up wishing that it used autotools. I suppose it shows that sometimes a few decades of polishing a turd does sort of work.
I don't think there will ever be a standard build tool, simply shunts to get the needed functionality from others. Eventually all build tools will exist in each other and the only interface will be recursion.
I especially like that one file allows me to develop on XCode, somebody else on Visual Studio and finally deploy on Linux/gcc. One config file creates native projects on all 3 platforms, no manual hacking.