I wouldn't know, but I'll give you a little hint, there are two ways to implement a better 'realistic' Pokémon storage but they have their own cons. Here they are:
1) Associate Pokémon in a habitat, preferably across a large area. Anyone remember 'Friend Areas' in PMD RRT and BRT? Yeah, something like that crossed with Oak's lab in the anime where he keeps all of Ash's Pokémon. This solution would be perfect and the Pokémon all are happy, but it lacks practical application. For one, a Trainer should travel all the way back to his hometown to meet his Pokémon. Secondly, the area required would be so huge that if every trainer in the world starts a journey, I doubt there would be ample space for everyone to dump (for lack of a better word) their Pokémon.
2) Putting a limit/ceiling on Pokémon capture capacity. Perhaps these Pokémon can accompany their trainer in their Pokéballs, but they aren't to be used in battle? Or maybe a trainer can only have six Pokémon at a time. This would ensure a VERY realistic journey, something like Pokémon Rangers where you have to release a captured Pokémon to let another accompany you. Cons being that it would ruin the 'Gotta Catch Em All!' motto since we'd have to frequently release the Pokémon/won't have room for special occasions. Again, a practical approach states that it would be very easy for a trainer to cheat and carry many Pokémon along with him/her (remember, the Bag seems to be able to store 999 Pokéballs, 999 Great Balls, 999 Ultra Balls and so on) but this would have been already possible by a trainer (albeit he has to do it in a Pokémon Center).
I don't know, these two methods are the closest things I could get to peaceful living for Pokémon and Trainer alike.