I was thinking, as I like the idea of adding the various pokemon according to their entries, that maybe some of this stuff could happen after so many days of playing when the players reach certain points. I think the coding would be a little bit complex but it would work like the Safari zone from the Sinnoh region.
As to working on the sprites if anybody has the original Gold/Silver/Crystal set, if you go to the daycare you can leave pokes there and you can use those as bases (I know it'll be like 16 bit graphics) should work.
Other than that I can't currently think of anything else at the moment.