This reminds me of an awesome story I once read (but now cannot remember the name of) in which a Trainer is trapped in the little segment of story leading up to fighting Brock, because the player keeps quitting when the battle goes wrong and restarting. Slowly, he starts to gain awareness of the situation, and... I don't remember the resolution, actually.
Actually, it's entirely possible that I dreamed that story rather than read it, but the point stands: that's the closest thing I can think of to this, and it was fantastic. Your concept is the same flavour of awesome, and I'd love to see it come to fruition.
I would have to point out, though, the high likelihood - assuming other people in the Trainer's universe are of the same independent mind as the Pokémon - that someone would find him and attempt to move him, or interact with him or his Pokémon. Perhaps that could be avoided by putting him in some kind of deserted location - or maybe you want to explore that, I don't know. Actually, you probably don't want to explore that; it's too much for such a tightly-constructed story as this one seems to be.