Via the JET Programme, you can work for five years. Whether or not your CO will let you work five years with them, well, that's up to your CO. But even if they only keep their ALTs up to 3 years, you can still apply for a transfer for the next year. (Speaking of which ... the deadline's coming up! Probably unnecessary heads-up to those of you who have been thinking about it.)
As for why ALTs leave, and when ... I can't find the declines disappointing. Every one of us has an amount of time that's right for us to live in Japan. And when you can't put the kids first, or when you can't be mostly happy going to work every day, or when there's just something else you're itching for, someplace you fervently want to be ... then it's time to go. Whether it's after one year, two years, or all five years. For every JET that steps aside, there's someone who wants to be here, ready to have their turn.
As for me, I'll probably be here three years. Then someone else will have their crack at my Tohoku penninsula of awesome ^.^.
2nd Year ALT
~That's my homeboy!~