Well that's a tricky situation. From what I can tell, there's five big pokemon right now when it comes to marketing/popularity that are the big deal of the Pokemon world.
1.) Mewtwo
2.) Eevee
3.) Genesect
4.) Lucario
5.) Zoroark
I'd say it's generally in that order as well. Mewtwo is the big thing because of the movie role, the big amount of merchandise circled around it and more, Eevee is big in the anime right now, is big in advertisement for the game and other media, and alot of merchandise, Genesect is being marketed with the new movie, partially marketed in other media and slightly seen in the marketing trailers for X/Y as well as Black 2/White 2 still being fairly recent, Lucario is used slightly in marketing other sources of media and the new games, and Zoroark is being used as one of the pokemon seen in the new pokemon game and more, including the fairly recent Black 2/White 2. But in short, it depends if Sakurai is looking to actually use two reps from the new movie, although I think Mewtwo means more than that.