I have long felt that the most efficient size congregation for discipling people for Christ is the middle-sized congregation (worshiping size somewhere between 100 & 200). This doesn't say that smaller congregations aren't "real" churches; nor does it deny the obvious programmatic advantages of larger churches. But in terms of the presumed "efficiency" of the bigger (esp. the "mega-") congregations, let's look at it this way.
Let's say you've got a 3-gallon pot of water, 2/3 full, simmering along, Every few minutes, you add a cup of cold water. The whole pot might cool a bit, but not much -- and soon, the whole pot is back on the boil.
Now let's suppose you want to heat more water than a cup every few minutes. So let's take a 30-gallon drum of cold water, 2/3 full, and build up the fire. Every few minutes, you add another cup of cold water. Sometimes, you add a cup of hot water. In either case, you will struggle a very long time to raise the temperature of the water to boiling point.
The "seeker sensitive" mega-church conforms to the expectations of those who are mostly secular in their outlook, saying that this way they can bring lots of 'em in. Those who get turned on to Christ can then be more traditionally discipled in small groups. But if the whole place is seeker-sensitive, then that sets up an ethos unlike what you eventually want them to embrace. Why should they "go on" to embrace traditional spirituality, when what they've got is so fun and comfy? It's like the "children's church" model where you have to keep demanding that the older kids start attending actual worship -- which isn't nearly as fun. And no matter how spiritual you are -- how on fire -- raising the temp on that much cold water takes enormous effort (as in, money & staff & facilities).
On the other hand, if you have a healthy medium-sized congregation, it can absorb one seeker after another in a small, steady stream. They get their questions answered instead of being overwhelmed by the churchiness of it all, and they meet real role-models right away. They turn into disciples, and then interpret the code for other seekers just stumbling in. And the congregation can continue to heat them up, because they are not overwhelmed by so many at once.
At least, this has been my experience.