I am becoming more convinced that discipleship can't be programmed on a large scale basis. I think that it happens on a more informal basis. What I mean by this is that individual disciples must become intentional about whom they will invest their time with for the sake of the gospel.
For example while I was in seminary I met each week with another man for coffee. We used various books to help deepen our relationship with Christ. This weekly meeting was discipleship. It was not a congregational program, it was one Christ follower intentionally investing in another person for the sake of spiritual growth.
I think the challenge is to look to see whom God is bringing into our lives.
Jesus called 12 men to follow him. His primary path for discipleship was living life with them, teaching along the way and modeling the kingdom life. I don't think we can improve on this basic model.