And packagers will everywhere will hate you for it.
I've recently written many GNU Guix package recipes, and packages using Autotools are the ones I tend to have the least headaches with. CMake and Waf are so-so I think, perhaps lacking in maturity, but I didn't have that much experience with them. Custom/hand-written Makefiles and ./configure scripts are the worst.
Just learn Autotools, get over the fact that they contain backwards-compatibility crud (that you can just ignore, or how does it hurt you?), and stop the FUD. Even if only targeting GNU and BSD systems, there is already enough diversity and library detection boilerplate to make it worth using a proper build system, and Autotools is the most mature one out of the bunch.
It's even more important for unconventional systems like Nix/Guix where software is to be built in very special ways, where hard-coded assumptions in build systems hurt, especially if a custom one; if it's a known one then even if hard-coded it will probably conform to some typical pattern of use of that build system so one can use tooling to automatically fix packages using that build system, and in the case of Autotools that isn't necessary in first place because everything is parameterized and flexible to hell and back.
Also please do use pkg-config. Like Autotools, it's not perfect either, but I could write another two paragraphs on how helpful it is in bringing consistency, toolability, etc. into build/packaging systems...