>Pokemon have the natural ability to shrink themselves down as a defense mechanism.
>Except they can't do it at will, because it's totally instinctual. And they don't do it when they faint or are about to faint. And also they can't do it to avoid being captured by things like cages or nets. And also they don't do it when they're being killed. And the pokeball forces that ability to activate to capture them. But only if they're conscious and more effectively if they're near fainting, except after they've been caught. Then it can be triggered reliably regardless of whether they're conscious or not. Also storing them in a computer is a completely separate phenomenon because they're not digitized into the balls.
It's still stupid. "The pokeball technology shrinks/digitizes them to capture them" is a lot simpler than some convoluted uncontrollable biological defense mechanism that's never used outside of the interaction with pokeballs