There's nothing inherently wrong with that, I think, except that Makefiles don't do well in a hierarchical setting;
Which is one of the main disadvantages of make that craft adresses.
and yes, I would tend to agree, one would like to get away from having to create a Makefile in every subdirectory.
With craft, you don't have to put a Craftfile in every directory. But you can if you like to, and if you do you _only_ have to put stuff which is specific to that directory in it.
Erm... I didn't know that. I've seen it used in a C++ project with little dependencies. But, yes, making it depend on autoconf again is not helping at all.
If you have little or no dependencies, you can use it without autoconf. But that is true of make as well.