> However, I note that makefiles are themselves little more than
> dependencies tied to shell script fragments, so clearly the shell and make
> are relatively tightly associated (indeed, make knows internally what
> characters are common shell metacharacters, and stuff like that).
Again, this is not a binary choice between plain old Makefiles and autotools. My choice is CMake.
CMake has its own scripting language which is portable across platforms (including Windows), versioned, and specifically designed for this use-case. Using the policy mechanism you can tell CMake "act as if you were CMake 2.6." Anyone with a version of CMake higher than or equal to 2.6 can then compile your project exactly as you intended. Shell scripts don't have any of these things.
Yes, shell scripts are appropriate for some use cases. But a build system is just not one of them. Let's use the right tool for the job rather than trying to explain how with a little duct tape, a plunger can be used as a hairbrush.
At the end of the day, nothing can make your code portable but you. But the build system can help you or hurt you. If it closes off platforms to you, like autotools closes off Windows to you, that hurts. If it forces you to write shell scripts to do everything, that hurts portability too. I've spent a long time fixing build breakages that resulted from autotools' poor choices. The question of what kind of Makefile.am or configure.ac a superintelligent Zen master who has studied AIX, IRIX, csh, tcsh, bash, zsh, dash, and every other shell out there might write is not interesting to me. In the real world, autotools = not portable.