I don't think you get treated poorly in general on the JET Programme. Quite the opposite. I think you get treated exceptionally well considering the circumstances. I think many participants need a reality check, though.
Enough of that.
You'll get sent where they chose to send you. I knew a girl who was sent to a city between Kobe and Osaka in the Kansai region, and when I participated (Yes, I am an ex-JET) I was sent to the boondocks. Hope for the best, but expect the worst. Make sure you bring an international drivers license if you go, whether you think you'll need it or not.
When you apply, there's a place for you to list your desired locations. Just be consistant and keep your desired locations close to one another. That's the best I think one can do.