I agree with you. In particular, the autopsy should have been done immediately in Texas as the Texas law enforcement community expected. There were medical examiners who were experienced in gunshot deaths in Dallas. It was Jackie, in part, who screwed that up, by both dramatically refusing to leave her husband's body and also insisting on going immediately back to Washington D.C. on Airforce One with the new President. She also accompanied the body to Bethesda for the autopsy that was performed there and then demanded that those doing the autopsy finish fast because she was tired and wanted to go back to the WH. Word was sent in to the people during the autopsy of Jackie's wishes that they finish up, and they did not do a really thorough job.
I remember the actual events, and some of the eventual doubts were caused initially by enormous over sensitivity to the Kennedy family shown by investigators. The autopsist destroying his original notes because they had blood on them, and he never wanted the bloody notes to see the light of day and add to the family's suffering is another example.
You really had to be alive then and remember some things that are not common knowledge now to appreciate how investigators bent over backward, and covered up gruesome details, to spare the Kennedy family (particularly Jackie).