Java by itself may not be the greatest shell language, because of slow boot times, lack of built-in libraries to work with the operating system, commands and files (I mean, there is even no way to copy a file in Java without resorting to creating two input and output streams and piping the data, yack!).
However! There are plenty of JVM-based languages like, JRuby(ruby), Rhino(javascript), Jython(python), Groovy or Grash, Bean-shell, etc. that work like shell languages and can run other Java-written programs. I would recommend you have a look at Grash that is probably exactly what you need.
Some of those language even have a way to pre-load JVM runtime to speed-up boot time (e.g Nailgun for JRuby), so that can solve the slow boot time problem. Also see this post for using Ruby(JRuby) as a shell language.