The most damning argument I've heard about the circumstances was that the PT Boats had finicky engines. This was a known issue, and there was a specific action that had to be taken prior to gunning them. I forget what the actual action was, but speculation is that the engines died because they attempted to gun the engines improperly, causing them to flood and die. This is hardly a dereliction of duty, but an error made under extreme circumstances, IF this is indeed what happened.
I have heard speculation that the 109 crew had hidden and were asleep. It is true that attempts by command to reach them by radio were unsuccessful for a period of time, but no one with any knowledge of the events has substantiated the claim that they were asleep. This appears to be mostly speculation based on the facts that it was around 0230 and that they were unavailable by radio.
It was a night time engagement and some of the boats were equipped with radar and some were not. The people running the battle ordered the radar equipped boats out of the area soon after the engagement began, leaving only boats without radar. Even if the radar equipped boats had simply stayed and provided the other boats with situational updates, it would have been a huge benefit.
Kennedy has been critized for turning off one engine and idling the other low. He most probably did so because bioluminensce paints a huge “shoot me” arrow in the water, that Jap aviators knew how to read.