CMake, SCons, maybe. This question was closed as not constructive, but the discussion looks reasonable to me:

http://stackoverflow.com/questions/600274/alternatives-to-au...

CMake was a step in the right direction, but it, too, suffers from thousands of under-documented options and fiddly behavior. In a former life I was tasked with maintaining a CMakeLists.txt for a project with multiple dependent libraries, binary blobs, open source dependencies that needed to get pulled in, and the whole thing had to be built for Windows, Linux, Mac, iOS, Android, and a handful of other lesser-known mobile platforms. I wouldn't wish that on my worst enemy.

It's not so bad. I have experience with two slightly different build systems based on CMake, which had to have customized toolchain definitions and build Cairo and WebKit. The Cairo build had a custom backend, which we integrated into Cairo's autotools. Cairo was driven using its autotools via CMake's "superproject" system.

https://github.com/roman-neuhauser/motoconf aims for that space, sadly it's very incomplete and dormant.

I wrote a simple PoC of a simpler way to achieve something similar:

https://github.com/SirCmpwn/scmake

It's definitely not something you should use, but I hope new things take a similar approach. It's small, give it a read. Here's a somewhat more complicated project that uses it:

https://github.com/SirCmpwn/libccmd

I think from a usability standpoint (both for devs and users) it's really great but the internals could use some work.

https://github.com/edenhill/mklove - mklove is end-user compatible with autoconf, without the nightmares.