I can't speak of the biggest obstacles but Clojure was bound to the JVM pretty early (hence the j) -- I personally have no real interest in getting off the JVM so I have not followed it close at all. Bootstrapping would be the obvious answer though.
There are no obstacles, rather there are several subtantial blocks of work to do, at least one of them non-urgent (rewriting the current Java compiler in Clojure).