Autotools is a huge pain in the ass for the dev, unfortunately I haven't found any alternative that didn't end up being an even bigger annoyance.
A decent, simple, easily customizable and portable C/C++ build system is still very much a unsolved problem as far as I'm concerned (and I've tried quite a few of them). At least autotools are supported basically everywhere.
By having autotools for the projects that need "everything" (legacy BS checks) and this leaner version for the projects that don't need them.
The same way there's vim and neovim without the legacy stuff.
CMake is faster than autotools and works fine with all the compilers talked about so far and all the windows compilers I know of.
Creating a CMakeLists.txt covering moderately complex build that links against a few libraries (but doesn't need and custom logic for moving files or other uncommon stuff) is normally just a few lines of code. Usually just one line of code per source file and per library (depending on how you feel about automatically including files this can be further shortened), then a little bit declaring the language and other settings. There are plenty of 10 line CMakeLists that can build large and seemingly complex projects.
As a rewrite using the same user interface but a completely different developer interface, there is mklove (https://github.com/edenhill/mklove). However, this just covers autoconf: you don't get the flexibility of automake. Also, I don't know how complete it is.
A rewrite just to speed up things a little is a bit useless. Autotools are not that slow. And if a rewrite was done, it would be a shame to keep the horrible syntax. What needs to be kept is
So why not get a tool with 1/10 the complexity and 1/100 the legacy stuff of Autotool, but the same interface otherwise?
People who need the old checks 100% could continue to use Autotool-old, people who don't care for such BS could use the new.