so the pokeball uses a scan of the animal, probably from the button on the front, or takes a DNA sample of the animal (so it knows how to rearrange it's atoms when its out of the pokeball) it stores all of the body as data/plasma/gas/energy/light except the brain (which is put in suspended animation) so its consciousness stays because if you don't keep the brain your essentially just taking atoms of it's corpse to make a clone, then you just shrink the distance between atoms in its brain and hold it in a cryostasis or plugged into the ball or held in a magnetic field, and people are wondering: "but how can you fit all of this into a ball including a generator to run it all", simple: shrink the distance between atoms of the machines and power generators and to keep it light because it will weigh the same as it did when it was big, make it levitate, preferably with magnetic fields using hyperloop technology, perhaps to improve the way animals/pokemon are stored in it, use nanotechnology and programmable matter/catoms so it can work better, perhaps use neuralink so you can train it or give it the memories of your pokemon from any of your game saves, this is a bit different to anyone else's approaches to making it work and different to the games but still it might work this way perhaps you can modify it to resurrect any of your recently departed pets (as long as most of its brain isn't gone)