White is supposed to represent Pokemon White players and you get Zekrom in the games (not saying that the manga is supposed to match the games, just pointing it out). So far, the Black & White chapter is seriously gearing towards a version favoritism, something that Kusaka has never done before, if ever. I know that in Generation V's case, Kusaka has to choose one version over another but at the end if both main characters could own their own corresponding Dragon-type then that would balance out the two versions. White could obtain Zekrom and then Black and White could use their dragons to fight Ghetsis. That could happen as early as BW but all things aside, it has to occur by B2W2 since N doesn't keep his Dragon forever in the games.

And just to point out, I have a feeling that the manga sorta corresponds with the anime sometimes. If the anime favors one version in an instance, then the manga will favor another. Like in the Jirachi movie, it centers around a former Magma member as well as Groudon. In the manga, it was Archie who survived and got to create a fake Kyogre, thus making Aqua survive slightly longer than Magma. Also, it seems like in the anime N will use Reshiram and Ash will use Zekrom. In the manga N is using Zekrom. Just pointing it out.