Look at the nginx configure scripts. They're hand-written, and modularized. Check for "foo"? There's a shell script. Autotools does the same thing via special-purpose autogenerated shell code.
That's why the configure script is 1000's to 10's of 1000's of lines of shell script. It's all auto-generated crap.
And autotools doesn't have the concept of bootstrapping. Building a C program? Great! Test everything with shell scripts. It might be more efficient to have C programs doing work, but no... it has to be the lowest common denominator.
Because managing multiple pieces is too hard. Why? Because there's no modularization.
I've used autotools for decades because everything else is worse. But I have a long-term deep-seated loathing of it which is hard to put into words.
I take it you've used CMake - could you explain in which ways you think it's worse than autotools? I agree it has concerning design flaws, but they don't come anywhere close to autotools' and I'd say CMake is overall dozens of times saner.
The difference is that autotools generates source distributions that do not need autotools to build, while a cmake project always requires cmake when building.
The problems broadly speaking are:
* Assumptions: autotools assumes that only a basic Bourne shell is available, and a basic make, and that make is a good way to build projects. All of those are questionable, and certainly if you get rid of the assumption that you're only allowed to use ancient tools, you could immediately make autotools better, if only by removing all the shell cruft. But then someone will complain because your project doesn't compile on SunOS 4 or whatever.
* Familiarity: When I'm packaging your project for Fedora, I will not be pleased if you've used some obscure or half-assed build system. If you're using autotools, I may dislike it, but at least I can fix things.
The second one is a difficult one, because until your build system gets popular, it will never be familiar, and us packagers will keep cursing you. Once it's popular, it'll probably be quite crufty because it has had to handle all the horrible corner cases that autotools can do now.