I'd say it's unlikely to happen - firstly, such a large game would be hard to implement properly (the level problem is just one thing by itself), and furthermore, Nintendo and all get more money by releasing a new region per generation (i.e. every few years), milking each game that sells millions of cpoies, than what they would get making one game with everything in it, which although would garner more sales than another game, would hurt future sales, take far longer to make, and end up being less profitable than what they currently do, I would think.
Not a bad idea in theory, but I don't believe this will every happen, really. (Unless Pokemon starts dying as a franchise and they get desperate to move away from their winning formula that has been effective for over a decade).
MMOs... don't see likely has happening either - leastways in the near future. Nor happening well if it ever happens unless well thought-out and all - after all, the attraction of Pokemon comes from the style it already is, not necessarily how or what a MMO may turn it into.