We're already starting to do that, though. We're working on 3D printing organs (whether they work or not is another thing altogether) so is it all that far fetched to say that some day we may be able to convert an entire creature into data instead of just an organ? It's all just information: this goes there, that here...Yes it would require a ridiculous amount of storage space, but it could (in theory) be done. 

I think the far more unrealistic part of the Pokeball is the fact that it can reconstitute that data into a creature. How does it do that? Where is it pulling the raw materials from? We could argue that they're converting energy into matter each time the creature is recalled, but that's pretty out there and (one would imagine) require a huge power source to draw from. 

I have seen theories that say Pokemon are actually just highly advanced digital constructs that inform a world-wide alternate reality game, that they don't actually have mass, just the appearance. However, I find that a bit hard to reconcile with all forms of canon (e.g., references to eating Magikarp, the use of Pokemon in construction). I guess you could argue that they're "hard light" holograms, but that's a bit hand-wavey for me, personally.

As for the impacts of the theories on the game we'll be playing... dot is requiring us all to have a background in biology, so the pokemon in the RP seem to be flesh and blood creatures.