Here are some of my more speculative thoughts regarding this subject.
The most important piece of evidence are the communication transcripts. For many years there were rumours that such transcripts exist. Finally, in 2003 the NSA released three such transcripts which cover communications between two Israeli Helicopters and the control tower. These Helicopters were sent to check on the ship shortly
after the attacks. (A side note, these were released after a lawsuit by Crystol, who is a federal Judge, and did his Ph.D. on this topic. His conclusion is that a serious of mistakes caused the attack.)
I have linked to the transcripts previously. From reading them it is clear that the control tower considered the ship to be Egyptian at first. Only later they start asking the pilots to find out the nationality of the ship's crew. I assume this is due to information they receive from the Israeli navy. (That is further reports from the torpedo boats.) There are several mentions of the US in these transcripts, including for the US flag.
After the release of these transcripts, there were claims that further transcripts exist. You can find them in several earlier posts in this thread. This leaves two options (please, no remarks about false dichotomy):
1. Other transcripts exist, but are covered up. The attack was deliberate.
2. There are no other transcripts. However, the existing transcripts were misinterpreted by several people. The Israelis misidentified the ship.
I support option 2. I think about this in the following way. Imagine you read a part of these transcripts but no one makes it clear to you that it refers to the Helicopters. You may naturally assume the transcripts involve the pilots which attacked the ship. Then, due to several mentions of the US, or US flag, you conclude that the attack was deliberate. Now, you are asked about these 30-40 years later, and naturally some of the details are changed by memory.
One of the points that lends support for my speculation is that the people who were more directly involved in recording these transcripts tend to be of the opinion that the attack was not deliberate. One is
Marvin Nowicki, mentioned earlier. Another is
Richard W. Hickman, which translated the transcripts.
All this is somewhat speculative. However, we have one piece of evidence which is not speculative, namely the transcripts of communications mentioned earlier, between the Helicopters and their control tower, taken after the attack. They are direct and clear evidence that the control tower (initially) did not know that this was a US ship.
Based on that my conclusion is that the attack was not deliberate, but rather due to misidentification. You may want to ask me what type of evidence would change my mind. This is a fair question, and I will therefore answer it in advance. I would need a contradicting piece of direct evidence. For instance one of the transcripts which are claimed to be missing. Alternatively, I would need some proof that the transcripts we have were faked.
I have taken time to explain my reasoning and conclusion regarding this incident because I do not expect any further information, relevant to my line of reasoning, to appear here. As a result I expect this to be my last post in this thread.