The key is to keep the project small. Once projects reach a certain size there's a whole ecosystem of bureaucratic parasites that latch on and begin feeding. "Purple suit" projects like this one are particularly prone to this problem since they involve three or four giant bureaucracies from the get-go.
As an alternate path, forget limiting project size, find harmless places to store the bureaucrats, and decide that success is worth whatever amount of money it takes.
I think that last element helps explain the Manhattan Project's success, rightly brought up by a poster above. They simply had to succeed and they were potentially able to tap the wealth of the entire United States to make it happen. Smart, motivated people + quasi-infinite resources: things can happen.
