No pokemon can be evil, the've stated that many times, the only Pokemon that comes close is my man Mewtwo, but even then he's just savage(most savage heart among Pokemon), so my speculation is that they will be the Pokemon of night and day and the plot of the game will probably be about the bad guys wanting it to be day 24/7 and visa versa for the other game.
You're right about that, although pokemon might attack people sometimes, but they're not evil, they just keep their living space. I'm sure it's the same with Zekrom (and Reshiram but this is unlikely).
Well the pokemon of the day and night is a good option, especially with Zekrom. As for Reshiram I'm not sure what the white color supposed to mean, because the day has very little to do with white.