From what I can tell, it's been around for a while, has countless modules, and probably is a better choice than Kit at this point, given the early stage of this project.
There are two main differences: (1) Kit is a project manager, while CCAN is a code archive, and (2) Kit modules are compiled libraries, while CCAN distributes source code only.
So, I suppose one would decide in favor of Kit because of its whole-scope approach. If not that, because CCAN looks quite hackish at first glance. From its homepage: "just hack whatever parts you want so it compiles in your project".