OK I will give my theory about JFK and the reasons why......
1-LBJ is under investigation for corruption from the Senate. The Kennedy's are not stopping it and LBJ's secretary said that JFK told her 3 days before that they were dropping LBJ from the ticket.This all went away when he became President.
2-Hide the truth of how corrupt the government is and it's tie to the Mafia and organized crime. RFK is busting the mob and also drug running through the south of the border. Laredo,TX was a big bust to stop this and the links to the Dallas Mafia,New Orleans,Hillbilly,the 5 families, whatever you want to call it.
3-The CIA extremists are ticked off. Allen Dulles wanted to be like J.Edgar Hoover and JFK fired him after The Bay of Pigs.So do you think Dulles on the Warren Commission was a impartial investigator?Talks of shutting them down probably had them freaking out as they had the Mafia do some of their dirty work.
4-The FBI's J. Edgar Hoover and his connection to the Mob. Yes J. Edgar Hoover got guys like John Dillinger,Maching Gun Kelly,and Bonnie & Clyde,but those were robbers not the Mafia... Why did Lucky Luciano slip bye? Why did Meir Lansky never ever get in trouble?? Why is it in the late 1950s J.Edgar Hoover said "There is no such thing as the Mafia,that's a myth" and a few years later it broke there was a Mafia and 5 big families. When the FBI used I believe Joe Rizzo to torture one of those redneck KKK guys to find out where the 3 teens in Mississippi(2 jews and 1 black) were buried in that swamp.
5-Sam Giacana(Chicago) & Carlos Marcello(New Orleans) hated JFK. Marcello had a big investment in Cuba with drugs and ,gambling,and prostitution and they wanted Castro out at all cost.Bay of Pigs ticked off the CIA but also corrupt types
6-No money to be made in peace. JFK stopped Cuba and then was going to get out of Vietnam. The big Military investors wanted to score big. Vietnam I believe cost the USA 200 billion
7-LBJ ordered it,Dulles set up the patsy and the hit men.The FBI covered it up with the cronies in the press.