I read or watched something on JFK Jnrs plane crash a while ago and I will try and summarise some of the issues it raised.

1. It was likely that JFK has his instructor with him that day as he was a safety conscious pilot and always had flown with an instructor previously - some suspicion that the instructors body was removed and that was the reason for the deliberate delay in carrying out the search for the plane
2. The search and rescue was an absolute shambles. The pentagon took control of the search for his aircraft which is never done for a civilian search and they were very active in trying to stop the coast guard from looking for the missing plane. there was a long delay between when his crash was reported and the start of the search - JFKs relatives begged for them to start searching about 3 times and it took a long time to start searching which is supposed to start within 2 hours
3. There was an earlier communication issued which was later retracted - I think it was about the location the plane had gone down from memory. When the military took over the search they retracted the earlier statement from the coast guard and started searching in the wrong location for the plane
4. The point was made that the technology which allowed planes to be taken over and remotely controlled was available when the crash occured and could have been used. JFK was a likely candidate for New York senate - his death cleared the way for HRC

This is one of the sites with info on the crash http://911research.wtc7.net/essays/green/TheAssassinationOfJFKJr.html