The Initiative perfectly answered the question, "What happens when you take a (supposedly) elite military group with a virtually unlimited budget and access to ultra high tech equipment and weaponry, and put them under the command of a group of civilians who can't even accept the terms, "vampires," "demons," and "werewolves,' for the creatures who they are trying to study when they should have been looking for more affective ways to kill them?" History proves again and again that soldiers can only operate successfully when they are commanded and led by soldiers. Put civilians, especially civilians who have no concept of what soldiers do, such as politicians or scientists, in charge and you create a situation known lovingly by every soldier, sailor, marine, and airman in the U S military as "clusterf*ck" (I bet you thought that Eastwood just made that up on the spot, didn't you? Actually, it came from a place called Viet Nam in the early 1960's) Then, in the end, after the inevitable sh*t has hit the proverbial fan, the scientists/politicians always have the same solution. "Bury it. Cover it over with concrete. Pretend that it never happened, and if it can't be covered up effectively, find some scapegoats (obviously, the soldiers that they had kept from doing the job right in the first place) to blame everything on, and release so many conflicting stories about what supposedly happened that the truth about what REALLY happened is lost forever. All of this, of course, while swearing to God above that they had opposed it from even before it was first suggested and fought against it throughout its planning, initiation, and operation, and that now history will prove that they were right all along.
Of all of the things that Joss did with this series, or either of his others, his portrayal of the Initiative, its mission, its chain of command, its operation, and its ultimate demise, was probably the most spot on thing that he ever did.