I came up with the story months before the fifth generation was revealed (early 2010). I also boycotted the fifth generation for a whole year after it came out to the States, and by the time I got to playing it this last Christmas, I'm already up to chapter 19 with a few more chapters to go. So it's too late to incorporate them into the story.
I hope so, too. We were promised his return, dammit.
I have no idea at the moment. Gonna try not to repeat my team on White (Samurott, Leavanny, Liepard, Swoobat, Simisear, and Druddigon).