While the official story is that a lone, disaffected Marine committed the crime of the century there were many more who had their reasons to wish to see the President gone... and they had the ability to do the job and cover their tracks after a fashion.

Federal Reserve – President Kennedy wanted to take money printing away from the Federal Reserve and bring it back to the government run mint.

Cuban-exiles – Wanted to remove Fidel Castro form power over their homeland and felt betrayed when the Bay of Pigs invasion failed and some of their fellow Cubans died because Kennedy withheld the air support of the operation.

Texas Oil Men – The President sought to end or at least reduce the oil depletion allowance that saved them millions in taxes.

Organized Crime – The President's father, Joseph Kennedy, who made numerous connections during prohibition called on some of these, like Sam Giancana in Chicago and Santo Trafficante in Tampa to help get John elected. To their dismay they found the President's brother, the Attorney General, executing an all out war on organized crime.  While Marcello did not support Kennedy, he did have his brother all over his crime organization.

Defense Contractors - Wars can be extremely profitable if you are not the one getting killed, and they saw an opportunity in Vietnam.

Joint Chiefs of Staff - thought he was weak on communism when he rejected their Project Northwoods to set up red flag events to use as an excuse to invade Cuba.  They also wanted greater involvement in Vietnam.

CIA – Because of the Bay of Pigs fiasco, Kennedy believed the CIA was out of control, running their own foreign policies, such as seeking to escalate the advisory action in Vietnam, while he was looking at withdrawing American soldiers, he vowed to break up the organization, and was in the process of generating the executive order to do just that at the time of his death.

Lyndon Johnson – Kennedy's amoral Vice President who hated the young, rich guy in the White House and who lusted after power.  He had connections to all the others with the common interest.

Deep state then... deep state now.