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In Black 2, I separated them by route caught; a box or two went to every few routes. For example, 19 and 20 go together, as did 4, 5, and 16 (non-Route areas get lumped in with the routes they’re on.)
Ever since then, I separated them based on what section of the Dex they’re in instead:
>X
Central, Coastal, Mountain, and National-only.
>Alpha Sapphire
Four groups of boxes for Hoenn Dex numbers, roughly by groups of 50 (i.e. quarters of the ’Dex; evolutionary families stay together.) Separate National-only boxes for each non-3 generation, since OR/AS gives you ARMIES of non-Hoenn ’mons.
>Both Moons
By which island Dex they appear in first: Melemele, Akala, Ula‘ula, and Poni. “Alola” boxes for ’mons either in all four is land ’Dexes or none of them, and then “National Dex” boxes.
In Ultra Moon I also give an extra box to the ’mons I name after Stardust Crusaders Stands
