The Delta Episode (the Rayquaza/Deoxys post-game story) is significantly harder. Trainers are Level 75–85, and the Legendary boss battles have perfect natures and fully optimized EV spreads.
Select "File" -> "Install CIA" within the Citra emulator, then select the 1.4 update file. Pokemon Omega Ruby 1.4 3ds Rom
First, a crucial clarification: