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I think that N's ideals is for pokemon to become perfect beings, equal to humans, and they must be separated from people in order for them to become that. I personally prefer N with Zekrom, because it makes sense when you consider the following points:
>N constantly talks about Ideals and formulas while rejecting the truth that's in front him throughout his journey (he admits to this at the end)
>N, and all of Team Plasma's, battle intros start with blue electricity appearing in both versions.
>N's favorite place is Chargestone Cave, a place filled with blue electricity. He even calls it a "Ideal" place for pokemon, if it weren't for humans interfering.
>Dark Stone would be sealed in Dragonspiral Tower around a snowy environment (Ice being supereffective against Zekrom, unlike Reshiram)
>Light Stone would normally be sealed in Relic Castle deep underground (Ground being supereffective against Reshiram)
It seems like that they wanted to go that way, but N and Reshiram is a popular aesthetic amongst fans, so they promoted it more.
