Right now, no organization at all. I have Good Stuff, Good Stuff 2, World Utilities (False Swipe/Hypnosis Gallade, HM slaves, Synchronize Ralts, etc), then EV Train (Pokemon that I'm done breeding but haven't trained properly), Breeding (All my Dittos, and then a bunch of Pokemon I want to breed), then Spares Project where I keep decent IV babies as bargaining chips if I need shit from my friends. Then the rest is a complete train wreck.
The way I want to do it is an advanced way of how I did it in Diamond and Platinum. In DPPt I had them in numerical order, all 493. Followed by a box full of forms like Unown and Deoxys. Shit was fucking terrible. But now I want to do it that same way, but much sleeker. For example, Box 1 would be Venusaur, Charizard (Y), Charizard (X), Blastoise, Butterfree, so on and so on, because I'm trying to train up a competitive version of every fully evolved Pokemon and Legendary, as well as some NFE or LC favorites. And I know the first 386 in the Pokedex fairly well so it would be easy to find literally half the Pokemon I'm looking for.
>>28125199I organized by Type in my original Sapphire. It was actually a lot of fun, until you see the barren boxes like Ice. Gave more room for Waters though.