That didn't come out right - I meant that sometimes people get the impression that make is incredibly complex because they look at makefiles generated by the autotools. Those makefiles are typically very different from hand-written ones.
Those makefiles wouldn't have to be as complex if automake only targeted GNU make. A lot of the messiness is there to support conditionals.
That's because conditionals are implicit in the underlying selection of targets. Trying to force explicit conditionals into the language gets cumbersome and ugly. You don't see explicit 'if's in Prolog, either.
I disagree. Writing multiplatform makefiles without explicit conditionals is cumbersome and ugly, mainly because the problem space contains so many exceptions. In this case, purism isn't really practical.