I think what you're talking about is part of a much larger pattern. Autotools imagines that the most important thing is the "user" in a world where people want to download your software and build it on their machine. They don't care (as much) about fast build times, the semantic clarity of the build files themselves, the ease with which one may change or extend the build sequence, test harnesses . . . Those are all developer worries.

They do care that the code can compile on their (possibly old) machine. They do care about the ability to include some features and not others (including their ability to not have to make decisions on this if they don't want to). And they certainly want documentation that helps them to achieve their goal (which, again, is to build the software).

The newer tools make substantial inroads in making the developer's life easier. If your software is not of the sort where people download it and try to build it (because it only ships as a closed binary, is entirely internal, etc.) then maybe that makes sense. But until all these fancy gadgets start seriously caring about the use case above, I'm going to stick with autotools.