Interesting. Are you talking about allowing users to write any Java code (including IO, reflection, and your game's classes) or just a subset of the platform?
At the moment, yes, but eventually I'll be putting in a security manager to minimize a players ability to cheat. I really want to give the player as much freedom as possible for the type of programs they can run, which is why I'm going to need a way to deal with the decision loop running for too long. But things might get a little nuts if access to reflection methods and game classes was allowed. Of course if I do wind up using a scripting language instead I won't have to worry about that, but I kind of like when games let the players cheat and completely break the game if they are clever enough, so at the very least I'm going to put in a way to disable or reduce the security, maybe as an unlockable.