I'm unsure how complex it would be. In PK3DS, there's a button called Mega Evolutions. I'm not sure what it's for, but hopefully you can change the item responsible for Mega Evos there. (I can't check what it does right now)
Next, in personalinfo, you can denote how many forms a mon has, as well as what position (in personalinfo) the next form is. For now, try something as simple as having the Arceus next form be the Mega Audino.
So, the end result of these two things, being an Arceus being able to Mega evolve into Mega Audino. If we can't even get the game code to do this, then we won't have to worry about models and textures and stuff.