Syntax is not intuitive? It's not bad once you've read the docs.
Complex Makefiles with huge included boilerplate libraries (e.g., the Android build system) are completely impossible to debug in any reasonable way? THAT is the problem.
As soon as you do anything non-trivial in your Makefile, you've created something that, when it fails, the reason will be COMPLETELY opaque to anyone who isn't intimately familiar with the ENTIRE program.
The implicit connections that a Makefile makes for building are great for JUST that part. As soon as you try to use them to write a program, you have to commit all manner of write-only-code abominations. I know because I've both DONE this and tried to debug OTHER people's code.
There is NO good way to debug Makefiles. And that alone means that they should be consigned to historic projects only, to be replaced by SOME kind of a better system.