Most probably it will be a side-game, it's too early for a new main series game... wait, I'm forgetting the floating possiblilty of the third version... but if there won't be a third one, a new Pokemon main series game would present a new Generation, and as I suggest in this message, it'd be far too early for the new Generation...
Everyone should know the 6th Generation of Pokemon shall be released worldwide on the 20th of December 2012, and the following day, Blademaster, DarkestLight, MeLoVeGhOsTs, Jeff, Charles Legend, Ultimate Charizard, Mikachu Yukitatsu and a bunch of other TPMers around the world will reach Uviridian Forest and encounter the 666th Pokemon and trigger literally the real APOKElypse.