A: Possibly. Could also be the GTS, or maybe a building he have yet to know about that will make a possible plot point into the story.
B: Sort of like an Amity Square-type area, don't you think?
C: IMO, it looks like it could be a Route 47.
D: For some reason, it looks sort of Mystery Dungeon-ish. You know, those friends areas of before PMDII? Could also be the Pal Park of Johto, or the Safari Zone reopened and for Generation III and IV Pokemon
E. It's Enju trees, If I'm not mistaken. Correct me if I'm wrong. But the unusual aura around it feels as though that they are clouds or something. If those were Enju trees, they wouldn't radiate too much like that, wouldn't it? They would just be normal looking trees instead of golden-colored desert like clouds. But it's near Ecruteak City. Possibly something related to Ho-Oh, or a new area.
Well, that's what I think anyway...