Seeing kick animations from Pokémon Stadium https://www.youtube.com/watch?v=Vpd47lTOjW0
I realized that to make aesthetic battle animations, Game Freak must add important areas to their 3D models/animations:
>Arms (punches)
>Legs (kicks)
>special area (special moves)
>Mouth/jaw (bites/special moves if lacks of special area)
>Head (head moves)

When the Pokémon will use a move, this move should have a parameter that call the animation that have the area that the move need, and then starts in the core of the area. Ie, if Blastoise has an animation where it prepare the cannons, moves like Water Gun should have a parameter that say "I need a special area so this is the animation that I need and I will start from the special area, which is in cannons in this Pokémon". If the Pokémon have two or more same areas the animation starts twice at a time (like in the Stadium kick animations when they use two legs). If some move hasn't an specific area, the animation uses a default animation and starts in the center (just like they currently do).

Now let's play a game. We make the work that Game Freak "haha don't know xD". Download a pic about a Pokémon and mark the five areas I said before.