(1) Castro did it, and the truth had to be suppressed to prevent a war with Cuba and the Soviet Union and to avoid the domestic repercussions that would have ensued from revelation of Kennedy administration assassination plots against Castro with the help of the mob.
(2) Kennedy was killed by a wide ranging conspiracy set in motion by LBJ using Cord Meyer, Frank Sturgis, E. Howard Hunt, and other CIA agents and operatives working free lance. To help carry out the plot, the conspirators recruited the Mafia based on their grievances against JFK.
Texas oil interests provided some of the financing and assistance in Dallas. Additional financing came from the Mafia and may also have come from cash provided by the CIA to the Cuban exile group DRE.
I tend to favor theory (2) because it accommodates evidence that I regard as persuasive: the stunning taped deathbed confession of E. Howard Hunt; the apparent fingerprint of LBJ operative Malcolm Wallace on a box on the sixth floor of the Texas School Book Depository; and the many indications of both Mafia involvement and CIA cover up.
LBJ's motive was his imminent dropping from the ticket in 1964 and prosecution for corruption in the Billie Sol Estes scandal. Cord Meyer's motive was that his marriage had been destroyed by Kennedy's affair with his wife.
As veterans of the effort against Castro, the CIA guys regarded Kennedy as having betrayed the Cuban exiles at the Bay of Pigs and betrayed the US through, among other things, irregular secret dealings with Kruschev during the Cuban missile crisis, fumbling in Viet Nam, failure to take action against the Berlin Wall, and a liaison with a German national who was a Soviet spy. JFK's philandering was a grave security risk.
The Texas oil interests -- principally H. L. Hunt and Clint Murchison -- hated Kennedy for curtailing the oil depletion allowance and as a grave threat to US national security and traditional domestic political arrangements.
The problem with a Mafia acting alone theory is that they could not be assured that they would get away with it unless they had sanction from the incoming Johnson administration and a full scale cover up based on LBJ's complicity.
The problem with a CIA guys did it by themselves theory is similar. In addition, for the CIA guys, allying with the Mafia brought in essential operational help, a more confusing trail for investigators, and deniability if the Mafia role was revealed.
Also, although anti-Castro Cubans were likely involved in the conspiracy and were angry enough to kill Kennedy by themselves, they lacked the ability to both penetrate Kennedy's security and to put a lasting cover up in place.
In this scenario, Oswald was part of a plot against Kennedy but was left holding the bag. The indications of a connection to Castro that run through Oswald are likely genuine but were contrived by the primary conspirators to provide an additional reason to limit the investigation to Oswald as a lone nut.
The Garrison investigation can be explained as a way for the Mafia to squeeze the CIA and Johnson. Garrison was deeply compromised and aligned with the Mafia and Carlos Marcello. As conspiracy theories swirled even after the Warren Commission, the Mafia and Marcello arranged the diversion of a crazy, publicity seeking DA making allegations against the CIA.
I suspect that the Kennedy family learned the truth of the assassination within a few weeks but judiciously preferred a useful martyr to impossibly contentious and politically disruptive allegations of a conspiracy. With RFK's death and the failure of Teddy Kennedy's campaigns for President, the family lost the prospect of exposing the conspiracy on favorable terms.
Oddly, some sympathy is due the CIA. Their people were used free lance by the Vice President to kill the President. The CIA then had to cover up the conspiracy and the role their people played lest, at the height of the Cold War, the US suffer a gravely damaging domestic political crisis and, in anger, blind itself by destroying its primary intelligence agency.
“the stunning taped deathbed confession of E. Howard Hunt”
Wow, a deathbed confession! How utterly convincing! Too bad he couldn’t point to any actual evidence while he was at it.