If I was going to actually work in the biz, then I needed to break away from what I was comfortable and play along with the rest of the kids.
Well, I don't want to work in the "biz", and this is a mere hobby project. On the other hand in academia quite a few people use java in AI related fields (see Weka, Jess or Pellet), and C++ is less popular. Also, I don't think Java programmers are less intrested in modding a game, it's just the AAA shiny engines are in C++/Lua for performance (shininess) reasons.
By the way it wouldn't make sense to make the core in C++, and create Python bindings, as the AI will be in user "scripts", and that's where the computational heavy lifting will be (especially in the offline learning mode; remember the goal here isn't shininess). Also, I'll heavily rely on the reflection API to create IDE like features ( Inspector widget e.g. for user defined units).