I wish standard (POSIX) Make would be sufficient but it frequently isn't. While some Make features from GNU and BSD Make made it into the POSIX spec (such as "include"), I frequently find myself desiring a more orthogonal facility to integrate output of external programs into Make builds. That is, by using POSIX Make's "VAR=`cmd`" syntax with backtick-quoted commands (or other shell evaluation syntax), you can define macros programmatically for incorporation into build rules as lazily evaluated text substitution variables, but you can use those only in build rules rather than in requisites or targets (where they get interpreted verbatim). A partial solution would be adopting GNU Make's eager evaluation syntax (VAR:=`...`) into POSIX.

OTOH, while I'm not a big fan of autotools internals (especially libtool), being able to run "./configure && make install" on tens of thousands of F/OSS packages is something I'd hate to loose. In fact, the extreme consistency in installation procedures (including use of pkg_conf etc.) and discipline in directory layout accross so many F/OSS packages is something I very much admire, given it's an unexpected outcome of a "Bazaar" style development model.