I guess Mossdeep City will have a place to switch between Deoxys's different forms, or should Meteor Falls?
I want to see a side quest that involves Manaphy and Phione, seeing as how they are ocean dwellers and Hoenn is tropical. It should take place on some new islands. Plus it should take a while to complete, as in longer than 5 minutes, probably 20-30. As for the side quest itself, maybe you can help Captain Stern, or someone else, locate the Temple of the Sea (at least a place based off of it) that requires you to ride a ship to some place in the middle of the sea, where a small Island is that has a small town that has a legend about a temple and Manaphy. Then you go from there to another tiny Island with another town that doesn't know about the other Island (they could be towns that are still living in the tribal days) that has a similar legend about a temple and Phione. Then you continue on an on until you reach an unusually deep area in the ocean, so you and captain stern, or whomever you are helping, decide to go investigate. The person you are helping goes down there in a submarine, and you dive down with a pokemon. Once you make it to the bottom, you find a bright-lit "town" that is in what seems to be a bubble of air, but is completely empty of any people. So, you and the other person go investigate the place, and discover the Manaphy and Phione.
I can't think of what could happen next or what the two legends the tribal towns have about Manaphy and Phione. This is just an idea.