The Pikachu was a happy mistake. In Emerald, if you do a scripted wildbattle like this:
wildbattle2 [PKMN] [LEVEL] [ITEM] 0x3, I found out that it plays the Kyogre battle animation before initiating the battle. In Glazed, the Scarfchu is in one of the 25 blank spots...I have reason to believe the intro animation changes depending on the species. I just made a tilemap with the Pikachu image, and replaced the Kyogre animation like you'd replace any image/tilemap combo.
As for the Elite Four, that's a built-in function from the games. In Emerald, A-Map has an option for "Elite Four 1", among others, in the "Battle Type" dropdown in the Header tab. That's what's responsible for their animation, BUT ONLY IF THE BATTLE THAT IS HAPPENING IS WITH A TRAINER ID THAT MATCHES THE EMERALD E4. If used for any other trainer, it defaults to the Champion's sprite, no matter what the other trainer's sprite is.
Hope this helps :3