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I like him with Reshiram. Aside from them looking good together, I think it would fit N to pick the Truth dragon. Like, he's bold enough to declare his beliefs as the one truth. Given how black and white his morality originally was, he'd be picking the "right" answer. The protagonist beats him because they have ideals, ideas and hope for a better future that can overcome N's rigid view of "truth."
Of course, this could be spun in the opposite direction - he picked Zekrom because he had ideals that could improve the world, while the protags smacks them down with the "truth." But I like the protagonist with Zekrom, and N with Reshiram.