I agree. We ought to be putting our effort into next generation build systems like CMake, rather than figuring out yet more ways to work around unfixable problems in autotools.
I've done a few conversions of projects from custom makefiles and autotools to CMake. In every case, the conversion was done in two days, and productivity was much higher afterwards.
I think some people are still wary of CMake because Linux distribution packaging folks are not as familiar with it as with autotools. But really, it's just a matter of time.