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In fiction it's always a struggle good against evil(sometimes evil is just a lesser good or a good taking the wrong approach) It's a metaphor for the struggle we all have trying to do the right thing. So yes the quest for enlightenment. You don't need to look at the imagery to see it's already there in the story.
Jirachi is the best pokemon http://www.youtube.com/watch?v=GODCCAOyCCs CRYAMORE FTW