This whole pokemon shrinking fiasco has made me realize that the people on /vp/ really are stupid and not put together the implications of a story written for children.
ALL pokemon can shrink naturally when they faint.
Some pokemon do it willingly if they learn minimize.
The pokeball takes this attribute and abuses it to find easy ways to store pokemon. The energy beam is basically a shrink ray. Naturally the pokemon would resist this and try to break out, thats why the pokeballs break.
Using modern technology theyve also found ways to turn pokemon into data which allows them to be stored in the pc.