Seriously!
What's the inside of those pokeballs like?
Are those pokemon aware?
Do they have a concept of time in there?
There's probably an explaination for it, but I doubt it would make any of us happy.
@King_Kindred: See, I always liked to delude myself into thinking that that is actually what ends up happening to the Pokemon. That they get transported to some sort of daycare-esque setting with the Professor or a place like it. At least in the newer games you can customize the boxes with a theme, so it's easier to imagine that're in more of a big virtual space than sitting in Pokeballs.
It was worse in the games because all of the PC pokemon would fall way behind the ones I carried on me in levels. So, I never bothered pulling them out again to train them.
George will just have to pay an annual fee for more storage space *CoughPokemonBank*cough* or pay a larger amount but have tedious transfering *coughPokemonBoxcough*
Panel 2 George (subtext): Really? You're going to point out the moral highground to me, mr. guy who hates fun, burned down a forest, and then freaking JOINED TEAM ROCKET the most EVIL people EVER? Really?
In the anime, the Pokemon are shown to just be shrunk down in the dark dimensions of the Pokeball (I remember this being demonstrated with Misty's Psyduck in an early episode, and there's another instance where Iris's Dragonite is shown sitting moodily in its Pokeball). In the manga the tops of the Pokeballs are transparent so the Pokemon can see out of its ball. As for the PC, in the anime it's shown that all of Ash's boxed Pokemon went to Professor Oak's lab, but that seems completely impractical for everybody's Pokemon.
My favored theory for the PC comes from the games. You can change the wallpaper in each box; I like to imagine that it creates a virtual space connecting all the Pokeballs in the box, based on what you set. Not that it makes sense for certain wallpapers, like the Team Plasma or Legend Wallpapers.