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I'm 80% sure that's where victory road will be and maybe even the legendary encounter. It looks like there is green beneath those clouds and it seems to raise higher into the clouds. And yveltal is a flying pokemon, so it actually makes sense to encounter either legendary there because of the grassy area and all the clouds, might be a way for yveltal to hide.
Victory Road is always next to the Elite 4. I'm pretty sure the castle to the left of 10 is the Elite 4, with the little area below being Victory Road.
But yes, the tree is most likely where you encounter both legendaries, depending on the game you have. Probably a different area to explore depending on the version. Y will have you climb to the top of the tree, while X has you going through the trunk.
From: P0k3m0nWaRR10R8 | #010
Which also covers the bottom of the map. My theory might still come true!
Yeah, I'm definitely seeing some mystery down there. It's strange that the map cuts off the bottom part of France though. Maybe there's more to explore after beating the E4?
I've also made a map showing what I think the routes will be, with the boxed areas being the areas you can Fly to. Keep in mind that just because the route is mapped out, doesn't mean you can't branch off of it a bit like onto the bridge to the right of Lumiose City, or the forest below the eastern-most snow city. http://imageshack.us/a/img5/7904/xyroutes.jpg
I've mapped it out on white background for clearer view of how the routes may look. http://imageshack.us/a/img32/7269/xyroutesmapped.png