Well....
1)Expand the secret bases,make them bigger
2)Match call/vs seeker trainers actually progress in real time
3)see
>>188408414)Hoenn styled contests are back and more polished
5)Top pokemon follows your ass like in Heart gold/Soul silver and if you talk to the pokemon,you enter in pokemon amie automatically
6)May/Brendan is stronger and you meet Wally in other places
7)Faster Dive speed and Dive caves are more variated
8)Use Emerald's resources like the Team magma/aqua battles in different areas[i.e. Aqua not using the meteorite in the volcano],Wireless adapter mini-games and other stuff
9)Deoxys event where you go to the moon,the island where you captured Deoxys in the original games is now Jirachi's island
10)Water pokemons are more variated
11)Keep the Regis puzzles and the cave where you open the Regis' caves will open a door that will lead you to a lv 75 Regigigas
12)Desert is bigger and has hidden stuff[this thing will make item finder useful] and the underground minigame will be here
13)STREEPASS SECRET BASES
14)Day-night times
15)Mega evolutions for some pokemons[i.e. Illumise and Volbeat]
16)Battle frontier is back and the battle points are more rewarding[i.e. You beat the pyramid without using items will give you more BP or win in the dome without losing a single pokemon or beating a Frontier brain will give you 50 BP then 100BP when getting the gold emblem[You get a double bonus if you dont lose 2 pokemons while fighting a Frontier Brain]
17)Make the gym leaders stronger or make some new game + hybrid like this: You can fight the gym leaders again but they are stronger and after that,you fight the E4 again and they are strong as shit but the champion is wallace [his team is lv 70-80] and Steven is in meteor falls and his team is all Lv 80-90 pokemons.