Autotools is a well tested and popular system there can be no argument about that. I've tried a few times to dive in and fix bugs or add features to the autotools build system unsuccessfully. And even after asking I was not able to find a single individual willing to offer advice. Autotools is an impediment for novice developers. I will stop complaining if some of the more experienced devs will step forward to document how we use autotools and offer to train others.
I'm going to have to agree with Aaron here. Finding a guy who truly understands Autotools is like finding a guy who can dowse water in a desert. Most of us C&P adjust and pray it works. Autotools are well tested and popular on Linux and BSD platforms but, you can count the number of projects that use it on Windows OS on one hand. A quick googling reveals none. Also this will most likely require developer to install Perl as well. Not a super big burden for developers since Bob is normally nice enough to bundle all the libs and extras up.
For the record I'm not saying Cmake is perfect but I can find more project using it truly cross-platform than Autotools. KDE being the biggest name off- hand and here is a List http://www.cmake.org/Wiki/CMake_Projects don't forget lib2geom uses it also.
I have nothing against btool either its pretty easy to setup and also works across platforms, I have less experience with it so I can't say much more.
Joshua L. Blocher verbalshadow