I find the ffd modifier to be too much of a generic shape for deforming. You can't change its shape from rectangular. Then the method of using a low poly version of the model as a skin deformer to deform the high poly model, requires quite a bit of setting up, that it doesn't feel practical.

I think a great solution would be to have a tool that, once selected, creates a deformation cage that hugs the surface of your selection (whether it be the whole object or a selection of vertices). On the rollout panel, the user can specify the number of control points, which would be equally spaced throughout the cage.

These control points could also be moved into position before the deformation occurs.