Organising those boxes

In my normal playthroughs, I put more significant Pokémon (like ones i've bred with a lot of good IVs or my main team members), i'll put them in boxes that I wallpaper with the legendary Pokémon on them. For example, in my main White 2, I have a box with White Kyurem wallpaper where I have nothing but (pseudo-)legendary Pokémon and members from my Hall of Fame team. Other than that, I don't really put specific members in different boxes - I leave most random ones wherever.
 
You have no clue how much I want a sort system in boxes. Sort by Pokemon name, nickname, Pokedex#, and so on.. that would make my perfectionist life so much better (as well as those who are catching things for a living dex)!

Right now I just sort of box Pokemon wherever unless they're members of my team, then I'll usually put them in the last box so I can find and withdraw them quickly when needed. Shinies have their own box with a "shinies" label so that's the only instance of me really organizing things properly. Eggs usually have their own box but that's only for quick access, again, since I hatch then all at once and then release or Wonder Trade depending on what I got. It's no biggie to me if I shove them in random boxes to clean up space.

Please give us a sort feature. :'(
 
I always keep my shinies separate from my other Pokemon. Other than that, I don't really do any specific box organizing. Sometimes I make a box for my original team members, or the ones that I journeyed with before completing the game.
 
I kind of have a weird heap/stack system when it comes to organizing boxes. That has been pretty useful in gen 6, as I was particularly active during this generation, especially in terms of Pokedex completion and breeding for competitive Pokemon.

The basic layout looks like follows:
- the first box is empty, unless I want to trade some Pokemon via manual trading, which is when I move the ones I want to trade to said box (prevents me from scrolling through all the boxes after every successful trade)
- from box two onward every Pokemon that doesn't solve a purpose besides filling my Pokedex, gets sorted by its primary type (except legendaries)
- after those come the boxes containing legendaries
- the last box contains all my Pokemon that serve a certain purpose ingame (ingame teams, Pokemon catcher, Pickup squad, etc.)
- the boxes before the job-box contain my "elite", basically all the competitive Pokemon I have
- before those comes the breeding section (future breeding projects, Dittos/Synchronizers, positive breeding leftovers (additional mons with all around perfect nature and IVs that I don't need for the moment))
- every other box between legendaries and breeding mons is empty
 
The only things I do that are particularly special with my boxes are separate stand outs into their own boxes. I have a Shiny Box, a couple Legendary Boxes, a Parent Box, a Team Box, and several IV Bred Boxes. Otherwise, I just kind of have them all cluster. It gets pretty spammy. Fortunately the PokeBank is awesome... though I don't use it a lot because it can be -really- tedious transferring so many Pokemon.
 
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