The Goddess will be the final villain of the whole game/series, so it won't be for a long time, but I do plan to give players that choice when the time comes.
Right now, the player is more focused on surviving in this new world he's found himself in.
About training, yes there will be a way to increase those other stats. I've got plan for Cecilia content, I'm going to be working on for future versions, that will add some more training options in.
As for James's conclusion, I've got a somewhat brutal ending planned for him, once Lily's content/story is done and I can move onto the next arc.