Ooh ooh pick me pick me!
I say we make the Leprechauns the evil masterminds behind it all! It'll totally work!
....Okay no. :P
On a more serious note, I was thinking about how we could tie the Epica and Aquias plots together (btw you still owe me a backstory explanation). The big idea I thought of was to make the enemy Aquias team tangentially responsible for making Annika's Pokemon vanish. Specifically I was thinking we could make the new Cloudsloom Gym Leader appear really nice and be an old friend of Annika's, but secretly be jealous and turn to EVIL (with a capital E).
As for kickstarting Aquias off, if when we get to that point, I was thinking about having Alvin challenge the Epica League, get trounced by another PC (probably Lian) and go off for the treasure. Unbeknownst to the other PC's though, he will actually find the treasure...only to get captured by the enemy Team and drop off the face of the earth. This will (assuming he hasn't made everyone hate him) cause the others to go looking for him. Nice thing about this is that it means we can have a rather powerful enemy team, as opposed to a group that can't use anything more powerful than a Golbat.
Just some ideas.