I imagine that some of the key areas in the game will receive expansions. I can really see Shoal Cave receiving an update. The dynamic of the cave itself it actually quite complex due to the tides and so forth. So I do hope that the games actually expand on this and make certain areas accessible at certain times, so that we can continue to find more exclusive legendary Pokémon. However, the number of Ice type legendaries is quite low. We have Articuno who could be a possibility, and Kyurem, assuming Regice won't receive a relocation. Hoenn would be a great place to see the legendary bird trio return though, but I'm sure it's unlikely due to their availability in X&Y. Though I do see Kyurem as a possibility in Hoenn's Shoal Cave.
I really hope they do something involving the Mossdeep Space Center, and Deoxys. Deoxys has never been available through the main game, you always had to retrieve the Aurora Ticket (FR/LG & Emerald) so as to go to Birth Island. However I reckon that given how the games like to make more story integrate with their legendary events; I'm hoping Deoxys will be available in-game. This is where the Mossdeep Space Center comes in. Predominantly useless in Ruby and Sapphire, it gained a larger role in Emerald. Team Magma attempted to steal the rocket fuel from the center. Other than that though, it's just sitting there with no real use. This is why I'm hoping that they will integrate some sort of involvement between it, and Deoxys.
Jirachi is another Pokémon who was "available" back during the time of Ruby and Sapphire, however it was another event Pokémon (Pokémon Channel, Pokémon Colosseum Bonus Disc). So I imagine that they'll pay homage to that in some way and make Jirachi available in Hoenn somewhere.
In addition to this, we also seen Mew on Faraway Island. Again this was another Japanese exclusive event. Given that Pokémon are being a lot more international these days, I believe we'll probably see Mew all over the world this time if they actually implement the event. Mew is one of the event Pokémon I can see making a return in some shape or form.
So assuming these, I am expecting Kyurem, each Regi, the Eon duo, the Weather trio (obviously), Mew (event), and Deoxys. I am thoroughly expecting more than that, but I'm going to wait until we have a map of the "new" Hoenn, since GameFreak having been calling it a "new world", afterall.