When you leave a pokemon inside a P.C. box do you think you somehow freeze your pokemon? That is not even close to what happens. Inside every pokeball is a completely different world. The P.C. is where all the worlds collide. Some pokeballs create a world to satisfy the pokemon while others just capture the pokemon.
Inside the P.C. most pokemon can explore everywhere. It is a place where your pokemon have their own journey. It's a journey no human knows about till now.