I came into the Bureau five years after the Miami shooting, and have met some of the guys involved. The idea that the Bureau scapegoated the whole thing on Jerry Dove's well placed but under-penetrating 9mm Silvertip is largely a creation of the gun press, apparently in reaction to the ammo tests that led to the adoption of the 1076 and different carry loads for the other calibers.
I can tell you that the entire shooting was mercilessly critiqued within the Bureau, and changes were made in a lot of areas, including tactics and equipment.
There were fourteen agents in the rolling stakeout that day, looking for the black Monte Carlo taken from a murdered owner a few days before. It was bad luck that the agents involved in the takedown had only two long guns readily available - both shotguns. McNeil elected not to use his, and has said since that he deeply regrets the decision. Mireles used his, but it was largely ineffective anyway. Other agents in the stakeout, who arrived after the shooting, had M-16s and MP-5s.
Now, every agent who wants one can have a shotgun, M4, or MP-5/10mm, and it can be mounted in a secure rack inside the vehicle rather than locked in the trunk. Body armor is required, and its use is stringently enforced (though it wouldn't have made a difference on 4/11/86 given the weapons used and the location of the injuries on the agents).
The Bureau took a look at the types of shootings agents are typically involved in, and designed a series of tests to make sure issued ammo met a certain standard. It is definitely biased toward deeper penetration, and that's fine with me. We don't issue ammo to other agencies or departments - they can use what they want.
As flop-shank said, its easy to take years to critique decisions made in seconds. Those agents knew Platt and Mattix were both hard core killers, based on their previous robberies. They identified them, made the decision to stop them, and killed both of them, though at a terrible price.