Thinking back on my earlier post, I think I believe the latter. If the Pokemon were in a state of suspended animation, how could they break out of the ball when you are trying to catch them?
Maybe it puts them in a dreamlike state and only the most stubborn, energetic pokémon are able to break free of the mental haze.
The apricorn pokéballs could be coated with potent sleeppowder inside. The metallic, high-tech ones could rely on radio frequencies that interfere with most pokemon's brainwaves in a way that prettymuch immobilizes them-- while turning their molecules into pure red energy. Perhaps the mirrors keep the energy contained as it bounces against the walls.
I'm not sure how the homemade ones from Kurt accomplish that same miracle of mass to energy in such a small space, but every craft has its secrets.
