So...Groundon and Kyogre.
In all of the excitement it appears that we've completely forgotten about them. But they are one of the only events that we know almost nothing about. What purpose do they have in the story, if at all? How will getting both of them get you Rayquaza? There are a lot of unanswered questions, and I no one's been asking about them.
My personal theory is that they will have a sub-plot dedicated to them in the Sevill Islands. Each game will have version exclusive landscapes based on the massive flood or drought happening there. Soulsilver will have vast rocky land routes, and the islands will become mountains. Heartgold will have a landscape like in Wind Waker, with huge quantities of water,and small islands with small little dungeons on them. Rayqaza will be located in Navel Rock. At first there will be a stone door with the two orbs on it, and when you bring Groundon and Kyogre it will open up.