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Okay, I dont know how this will sound but I spent like 4 hours sorting my boxes last night.
If possible Ill do by number. right now bulbasaur does occupy my first spot.
Then after the general caught population I have them sorted by Breedstock, Dittos with marked and Maxed IV's and then The pokemon I have special bonds with, like the pokemon I ran through the game with or my first caught pokemon. stuff like that.
after that I have all my fully trained pokemon/ frequently used Pokemon such as HM slaves and Egg warmers.