Story's alright, maybe you could add a team that worships the dark silhouette (darkrai i assume. ;p) and believe that all the people are succumbing to nightmares b/c darkrai's wish is for all trainers to fall into deep slumber for the team to steal all the pokemon and give it to darkrai as sacrifice so he could feast on more dreams? (just an idea)
Some more lore? Like you could make one up, cause Palkia and Dialga/Groundon and Kyogre/Reshiram and Zekrom had some interesting origins which give a little tint of mythology, so you could maybe add the origin of Darkrai -- altho that's a 50/50 idea as the whole point is that the silhouette is unknown soooo....lol. xD
Anyways i can't say much about the mapping etc. as i hven't seen much, but I can say that it's good to see battle animations in the battle system, as most rpg maker pokemon games neglect it, and, well, i love battle animations.
I suggest spicing them up as the animations arent really smooth and lack the "feel" of the impact, if you know what i mean.
Other than that, battle looks pretty solid. keep the good work up.