If there is a third version, and there most certainly will be given enough time, they'll do the same thing for Kyurem as they did for Giratina most likely: level it down considerably, give it an alternate form, and adjust the plot accordingly towards these adjustments. Don't know how exactly they'll adjust the plot. Maybe a 6 vs. 6 double battle with N and Ghetsis with both of them using Reshiram and Zekrom against you and one of your Rivals, most likely Cheren, battling alongside you. Who knows?