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.