A virtual reality Pokemon world doesn't seem to far off, we just need the AI capabilities and we're set! A holographic Pokemon buddy doesn't seem too far fetched at all. Unfortunately most games are focusing on GFX instead of AI or gameplay these days though.
As for biologically "real" Pokemon? I just don't see that happening, unless the human race learns how to create custom lifeforms with genetic code. If that WAS possible, I'm sure we'd have a lot to worry about..and Pokemon would be the least thing on people's minds.. ;