That's pretty imaginative. Obviously a great deal of thought went into the OP. A Pokemon MMO might give those of us who haven't played since the 2nd-gen a good reason to pick it back up. I would love to see some realtime combat in a Pokemon game.
Link in a futuristic setting doesn't really gel. It's almost corny. Link, with trusty R2 unit to aid him and lightsaber in hand, learns that Ganondorf (who is now encased in a life-supporting cybersuit) is actually his father. Oh, almost forgot. Zelda is his sister, and Saria randomly appears as a blue spectre to give Link encouragement.