I wouldn't even count that since it's not directly from Emerald, it's just a new different thing they added so Rayquaza has some more relevance. The one thing off the top of my head they did take from Emerald is that when you fight Wallace during Delta Episode he uses his Emerald team. Oh yeah, and Prof. Birch gives you one of the Johto starters in the post-game, though the condition for it is different (just completing the main story, while in Emerald you had to complete the regional dex), and in ORAS it's part of him also giving you one of the Sinnoh and Unova starters too so everyone Pokemon could be natively obtained in Gen 6.
Otherwise yeah. There's none of the changes to the Gym Leader's teams from Emerald (especially bad for Liza & Tate), none of the small changes to various routes and the trainers within from Emerald, nothing from the Battle Frontier, none of the Emerald-exclusive characters like Juan. And y'know what, even if they weren't going to have fully customizable characters like XY, it would have been cool if you could unlock the original RS and Emerald outfits to wear.