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Skies is far better. Other than the things mentioned above, skies came out during a time when there were other jrpg options and it was popular and it was still good!. Ni no kuni came out during a time when jrpgs are nowhere near as popular and it kind of brings back that nostalgic feeling most people used to get when playing them.
Skies has better everything just about.Story, battle system, world, humor and replayability.