I saw a talk Mike gave on Luajit last week, and one thing he credited Luajit's success on was that it was working on a rather high abstraction layer. Stuff like the loop optimizations and alias analysis work because the optimizer can essentially understand the code at a fairly high level, and is somewhat specific to Lua. When dealing with java translated to jvm bytecode naively translated to lua source you lose much of that context. (And at the time he didn't seem too convinced about using luajit as the backend for other languages.)
But even if you ignore the loss of context, I'm sure that various luajit limits would get hit with real life Java code. E.g. I'd guess there's a fundamental 65k limit for the number of constants and bytecode instructions in a single function.