Answer
It now seems like a small set (100ish) of genes is responsible for many or most large scale developmental changes, the second view listed in the question. This is easier to see happening/more obviously probable rather than the accumulation of many needed changes in a large number of genes.
Work Step by Step
It takes time, a long time, to accumulate a number of evolutionary changes needed for a particular phenomenon. It is much more likely for this to happen in a relatively small set of control/regulatory genes than in many, many genes needed to explain phenomena.
