I think it's a memorable experience that is worth indulging in at least once. I would recommend that you go for a somewhat luxurious ryokan for your first experience. That way, if you find that you can't tolerate the somewhat regimented arrangements (eat now, bathe now, sleep now), and sleeping arrangements, you know that you have given it your best shot.
And - personal preference - I like rural ryokan with an old world feel. I think that spending an evening at a historic inn in a little town like this and is "must do" but YMMV - http://www.japan-guide.com/e/e5854.html