I am thinking on putting at least something in a separate area rather than everything on main area.
I think that the feature that best fits is a ticket/boat sample event with two tickets to two islands with legendary pokémon. The first only have the legendary pokémon, the second have a mini-dungeon with the legendary pokémon at the end. About the pokémon I am thinking in Latios/Latias (like the event in Emerald) and Deoxys (Speed Form). Starting in Platinum, if you don't caught the legendary pokémon (defeat it) it return after you beat the E4 event. The pokémon continues returning until you caught it. How about making a sample legendary event with this, but maybe another event instead of the E4?
Deoxys would be a good example, as there can also be meteorites to inspect which change its form. The other Pokémon can be something like the Shiny Gyarados (i.e. use a script to force it to be always shiny). One can return every 24 hours, and the other can return upon setting a certain switch (which is then unset).
The only problem is that there's currently no support in Essentials for changing the Town Map's graphics during a game. I'm not entirely sure how best to go about it (specifically, how to make it easiest for the user to use).