This question is a testament to why Black and White were so well constructed, story-wise (and a nice, if cheesy little nod to the sentiment - "it's not all black and white").
You can quite simply approach it from either side. I played White (first), and so for me, Reshiram fits better with N. If we must read into it, N believes that his outlook is the tru path for the Pokémon world to take: humans and Pokémon ultimately don't belong together because humans use/abuse Pokémon for their abilities. The protagonist uses Zekrom to project the ideal world into existence; where Pokémon and humans can co-exist in harmony.
But it works if I flip it. N can use Zekrom because his belief is that, in an ideal world, Pokémon will receive the respect they deserve by living separately from humans. Whereas the protagonist will use Reshiram to represent the true world: Pokémon and humans are meant to exist alongside humans, to help one another.s
I'm not saying anything OP didn't already know, but just wanted to expand on why the story/concept is well-crafted. My choice is, N uses Reshiram, and protagonist uses Zekrom. A little-referred-to aspect of the pair is that Reshiram is part Fire type and reminiscent of primitive/traditional tools and methods, whereas Zekrom is part Electric type and represents futuristic technologies. I like the approach that N is trying to revert the world to a point where people and Pokémon remain separated, whereas the protagonist is fighting for the future, where people and Pokémon coexist.