Building your Army
But how would you go about capturing these Pokémon in the first place? There are a couple things about battling and capturing Pokémon in the wild that I find quite irksome. The fact that these creatures, no matter what their variety, will always attack you when you come near doesn't make any sense to me. I would imagine that the vast majority of Pokémon would flee from a trainer crashing through the underbrush. I know that there are some more realistic ways of luring and capturing Pokémon in places like the Safari Zone, but I don't think these methods need to be confined to special areas.
There's also the fact that capturing Pokémon in the wild is the natural beginning of any Pokémon Trainer's journey, but it is portrayed in a horribly barbaric fashion. The main pastime of the Pokémon universe's occupants is the violent capture and enslavement of innocent forest creatures, which are then forced into mortal combat against their will. For such a cheerily portrayed world, the underlying truth behind these Pokémon's cruel fates is callously disregarded.
What I'd like to propose is a system where Pokémon are no longer "captured," but are instead "recruited" through non-violent means. I'll try and illustrate this system with an example. Let's take the role of Ash again, as he takes a walk through a forest. He may periodically see Rattatas or Pidgeys running through the underbrush or flying through the canopy. Let's say he wants to add a Pidgey to his lineup. His strategy would mirror that of a birdwatcher in the beginning. Follow a Pidgey to its nest, and attract it with bird calls. Perhaps from a flute that he acquired at a nearby shop. Once he has its attention, he baits it with food to draw it near. He may do this for several days, gradually building trust with the bird until it will happily sit on his shoulder and eat from his hand.
At this point, the bird's "friendship level" would be high enough for it to be recruited. A Pokéball could then be tied to this particular Pidgey, and it would be able to be "summoned" whenever that Pokéball is selected in battle. Pokémon wouldn't actually LIVE in the Pokéballs any more; they'd live in the wild where they were originally found. Using a Pokéball effectively teleports its linked Pokémon to your side. A key feature in this is that the teleportation is based upon the Pokémon's actual desire to be summoned. If you never use a Pokémon or are generally cruel to it, it might not answer the call from the Pokéball. You'd either have to return to where that particular Pokémon lives and befriend it again, or choose to permanently sever your connection with it.
There could be some other methods of befriending Pokémon, using the prior system as a basis. Let's say there's a Nidoking desperately trying to save its children from a forest fire. If you whip out a water Pokémon and save the small Nidorans, the Nidoking would be indebted to you and form a Pokéball pact with you right then and there. Or maybe you find a lone egg in the desert, and take care of it until it hatches. The baby Pokémon that hatches could believe that you're its mother, and boom. There's another Pokéball pact. Other more humanistic Pokémon, like Mewtwo for example, may choose to form a pact with you after you defeat them in battle.
The whole idea here is that the system becomes a lot less video-gamey and a lot more believable. No more being jumped by rabid Rattatas in every field you walk through. No more knocking Pokémon out and not being able to capture them because you can't limit the power of the Pokémon you're trying to capture them with. Fewer systems based on stats and leveling up and more systems based upon actual trainer/Pokémon interaction.