The problem with a programmes based approach to church is that it too often removes people from the communities in which they live and work and transfers them into a church community disconnected from their ordinary lives. Programmes can simply serve to keep people busy, too busy in the end for any real involvement in God's mission.
But we can't stop having programmes! Programmes help us organise ourselves, they help us strengthen areas of weakness and encourage areas of strength. Programmes are good provided the programme serves the purposes of the church and doesn't distract from it.
The second problem with programmes is that they don't always work. In a long term study carried out through the Willow Creek Association, they found that no matter how good your programmes for discipleship might be, very few people were actually being discipled through them. The people who were actually growing in their relationship with God were the people who were actively involved in the ministry of the church, and I'm not just talking about weekend services and internal church stuff.