Considering how FRLG and HGSS came out, it's safe to assume that ORAS will be Emerald remakes with the version differences of RS applied to them. In that case, I would like to see them "pull a BW," so to speak.
First time through, you fight Wallace as the 8th Gym Leader, and Steven as the Champion.
Defeat Steven, watch the credits roll, and Juan replaces Wallace as 8th Gym Leader. Wallace replaces Steven, and Steven goes off to Meteor Falls with a stronger team like he does in Emerald.
I have nothing against Wallace, and I love him as a Gym Leader. Juan is pretty cool as well. But having an all-Water Champion along with an all-Water Gym (and the final one, no less) severely reduces the challenge and was not a design choice I enjoyed at all. I think the method I described above helps keep things consistent between both RS and E, and gives the main part of the game a bit more challenge with diverse types amongst the league members.