1. Lack of adption: It's not widely used yet. Implementations for few languages.
2. No formal spec; the "spec" is very imprecise and seems to try very hard to leave as much as possible to the implementation.
3. The spec is very, very Java specific. No clear separation between "core HOCON" and "Java extensions".
4. It probably doesn't lend itself well to automatic changes in a way that preserves structure of an original file (-> without just rendering out JSON).
It's clear that HOCONs only real focus is being easy to edit manually.
It's a nice idea, but it's definitely not the long term solution we need.