Quoted By:
N - Zekrom
Hilbert - Reshiram
N was raised by Ghetsis, since he was a orphan child, to purse ideals while being purposely denied the truth his whole life. Everything about him hints this. His sheltered backstory, his fascination with mathematical equations, his admiration for Chargestone Cave and even his(and Team Plasma's) battle intro involving blue electricity. It makes since that he would purse Zekrom, the being of ideals, over Reshiram.
Meanwhile, Hilbert spent his whole game seeing things as they are, aka the truth. When he encountered Team Plasma at the Dreamyard, he was immediately shown their true nature, including their spokesman Ghetsis through a dream, and they've been given him glimpses of it ever since. He, unlike N, grew up in a normal environment surrounded by friends and family and thus, knows what people's relationship with pokemon are really like. That's why Reshiram, the being of Truth, fits him more. Plus, Ghetsis wouldn't bothered with getting Reshiram as he probably fear that it'll expose his ambitions to N and ruin his plans.
