1.Battle Frontier, including Artisan's Cave.
2.Gym Leader rematches.
3.Juan(Wallace's champion team is present in Delta Episode)
4.Rayquaza centric storyline.
5.Mirage Tower, Battle Tents, Desert Underpass, Terra Cave, Marine Cave, Faraway Island, Navel Rock, and Birth Island, as well as Jagged Pass hideout of Team Magma are not present. Deoxys can be battled in the same way as in Birth Island, though.
6.Pokémon Center Ladies.
7.FRLG Move Tutors.
9.Altered encounter tables with Poochyena replacing Zigzagoon.
10.e-Reader and GBA Wireless elements.
Missing elements from RS:
1.Female Psychics and Triathletes.