It's not entirely true that a replacement for autoconf would just have to be a better autoconf. You don't need a solution that works at all like autoconf (doesn't even have to generate code at all). You can avoid MUCH of what autoconf deals with by writing portable code and following some sane strategies for constructing include paths and selecting library files. It's just that when you do that, you have to solve all of these problems yourself, while the autoconf library has already been battle tested on a wide variety of platforms... a level of effort that would be hard to replicate.
Agreed, well said. I didn't mean a literal better autoconf, I meant that the attempts to replace it have rewritten the problem to a lesser, simpler one.