>>48830539every new game I build a living dex on it, so starting with box1 I always go by Nat number + forms + physical differences so it ends up something like this:
for forms I go with:
Burmy (grass), Burmy (ground), Burmy (trash), wormadam (grass), wormadam (ground), wormadam (trash)
for physical differences VISIBLE on the thumbnail sprite:
Shellos (pink), Shellos (blue), Gastrodon (pink), Gastrodon (blue)
then I use the last box for my competitive Singles pokemon.
then the second-to-last for my competitive doubles pokemon
then the one before that one for my army of hexaperf foreign Dittos (all holding destiny knot)*
then the one before that one my army of Synchronize Abra/Kadabra/alakazam* with every nature
then, and only If I have the space I keep an extra box for every shiny I manage to find on that game before I need space and move them to the game with the most shinies on it (which I also sort in the aforementioned way
*- only on the latest game of the gen