In "The Plan", why did Hilda get so very little thought by Ghetsis, while we see the battle with Alder and what Alder's words do to N? Simple, Ghetsis's master plan was built on defeating Alder, not some random girl. He let her go past him because he was absolutely sure she was not a threat to his plans or N. He probably even assumed that N dropped his cube from Alder's words just because of Alder's words, and not because N got perspectives of others while traveling, especially from Hilda, that might make him question his ideals. It would be this obliviousness and Pride that would lead to Ghetsis' potential downfall.
Why is Hilda with Reshiram and N with Zekrom? Simple, N wants an ideal world while Hilda is going to show him the truth of the world that stands. It would be the truth that would show N the error of his ways, and make him realize Ghetsis' true plan.
A lot of shots of those around Ghetsis, like N, Anthea, and Concordia, sound off. N gives constant lowered stares and the girls talk in a strange and stoic monotone. They don't look like real people or sound like them. This is also Ghetsis we are following, who doesn't see N as a real person but a tool and pawn. He's dehumanizing them mentally. Note how a person he thinks of even less than his tools, Hilda, and someone he has to give more thought to than his perfectly set up pieces, Alder, don't have this problem.
Why is N so quiet? He's normally a Motor Mouth, speaking very quickly, but here, he has exactly one line of dialogue. It's likely a deliberate choice in this adaptation: the protagonists are all silent, save for a voice grunt or two. N draws parallels to the protagonists throughout the series, complete with Signature Headgear. Like most of them, he's also worthy of being able to summon a Legendary Pokémon, and if it wasn't for the whole Team Plasma deal, he'd be just as heroic as them.
In "The Discovery", Elaine is able to beat Green and Trace in finding and capturing Mewtwo despite showing up last. Given that she didn't participate in the race, she was able to find an alternate, easier way to the Genetic Pokémon.
