I LOVE Hoenn! I think that if they do remake Ruby and Sapphire, the graphics should be improved to at least D/P standards (hopefully B/W, but that takes lots of space). I love pretty battle animations and think they really enhance the game.
If they added 4th gen. Pokemon, there would be more variety and the Elite Four would have a more, "elite" team. I think they would keep Wallace as champion and follow Emerald's gym leader/elite 4 pattern. Also, I think May/Brendan should be able to choose if they want to act as the hero/heroine, help Team Magma, or help Team Aqua. THAT would be awesome. In past games, you ALWAYS had to be the good guy/girl and save the day. If you chose to help a "bad" team, you could have certain chances in the game to contribute to either team or not, to determine whose side you were on. For example, if you gave the Devon Goods to team Aqua instead of Capt Stern, they could pay you a sum of money and thank you. And after 3 times of helping Team Aqua, they gave you a uniform and gave you tasks to contribute to their cause. ( Or viceversa with Team Magma. However, if you did follow a hero's path, the game would have a happy ending, because when one power {water or land} overpowers the other, there are always consequences. )
That's just what I think. :)