The difference I see is that Autotools is mainly useful for handling differences between various Unix variants, which isn't a concern now that commercial Unix i

The difference I see is that Autotools is mainly useful for handling differences between various Unix variants, which isn't a concern now that commercial Unix isn't really a thing besides Mac OS X. CMake doesn't have the years of arcane knowledge about dozens of Unix variants that Autotools does, but it lets you target Windows using the native tooling as opposed to having to do all your development in Cygwin, and it automatically generates IDE projects so you can use IDE provided tooling like debuggers and profilers. Personally, I think this is a more compelling value proposition than what Autotools offers. Obviously, if you're fine with using a text editor and GDB and for some reason need to target SunOS, SCO UnixWare, 386BSD, A/UX, etc but not Windows, Autotools is great for that use case and you should stick with it.