"On the other hand, there aren't any better alternatives, so I'll just go cry for a bit."

Indeed. As the person who cross-compiled a ton of libraries for Windows (http://fedoraproject.org/wiki/SIGs/MinGW) I can tell you that autoconf and CMake are the only build environments which handle cross-compilation properly and transparently.

BTW CMake is not better or worse than autoconf, just different.