I find autoconf to be good at its job - building a standalone script which runs micro tests - and still use it, but that automake and libtool add very little value for the reasons you described.

I do agree that m4 is rather unpleasant to write, and that the resulting tests are too slow (often because user defined macros do a poor job of cacheing) but I also think that these things could be addressed (newer macro languages, bundled or threaded micro-tests) while still preserving the good bits of autoconf.