Stick with automake. Seriously.
I think it might actually be worse than autoconf in every way, which is surprising considering how bad autoconf is. The handwritten non-macro-expanding not-much-autogenerating configure/makefile in ffmpeg/libav/x264/vp8 is easier to deal with than either.
To me, it's not perfect, but it's pretty good. Then again, I'm known to my friends as "that guy who knows automake" :-).
A lot of automation routines designed on unix-a-like systems involve creating short lived processes with reckless abandon because creating and tearing down a process in most Unix environments is relatively efficient. When you transplant these procedures to Windows you are hit by the fact that creating or forking a process there is relatively expensive. IIRC the minimum per-process memory footprint is higher under Windows too, though this doesn't affect build scripts where generally each process (or group of processes if chaining things together with pipes and redirection) is created and finished with in turn rather than many running concurrently.
This is why a lot of Unix services out there are process based rather than thread based but a Windows programmer would almost never consider a process based arrangement over a threaded one. Under most unix-a-like OSs the difference between thread creation and process creation is pretty small so (unless you need very efficient communication between things once they are created or might be running in a very small amount of RAM) a process based modal can be easier to create/debug/maintain which is worth the small CPU efficiency difference. Under Windows the balance is different: creating processes and tearing them down after use is much more work for the OS than operating with threads is, so a threaded approach is generally preferred.