I think Javy's problem at the plate is similar to what Jeter's problem was in the field: he has poor reaction reflexes. Jeter had poor range not because he was slow or nonathletic, but because he took a few milliseconds longer to recognize where the ball was going, and then reacting to it, than the average big league shortstop, which was enough to result in a whole lot of pasta diving. Similarly, Javy is a good-enough hitter when he gets to the ball, with decent line drive ability and above average EV, but I believe Javy can't let the pitch travel much before committing to a swing because he can't react to where it's going when it gets too close to him. In this respect I would bet he is in at least the bottom quartile of established hitters.
If this is true, I don't believe it's the kind of thing that can be fixed—reaction time is baked into his physical tools. The goal then becomes get enough out of the positives (hard hits, good base running, good defense, with the occasional eye-popping catch or slide) to more than offset the negatives that can't be helped.