There's no way of knowing which theories were true-only God and the people involved know. But of all the theories, which ones (or combination) are the most likely true?
There definitley were cover-ups, not only because of what happened with Lee harvey oswald, but also because of other facts.
https://en.wikipedia.org/wiki/John_F._Kennedy_assassination_conspiracy_theories
Read those parts of the article.
Allegations of witness tampering, intimidation, and foul play[edit]
Alleged witness intimidation
Also, I believe the Mafia was definitely involved. The mafia didnt like him because his father was connected with them and used that money to help JFK get to power, but his brother went after them. It makes sense to believe the theory that the mafia hated Kennedy because they felt betrayed. Some Mafia people even claim they were involved.
http://www.newsmax.com/Newsfront/john-kennedy-assassination-confession-mafia/2014/11/20/id/608736/
The mafia had connections with many other famous people, including musicians like Sinatra, so its not far fetched to think JFK had connections with them.
I believe different groups were involved with it, but I do believe any one of the conspiracy theories that involve the government and JFK (including the "shadow government" and the military) are probably true. The problem with the New Orleans and Cuban theories about Kennedy is that it doesnt make sense how the Mafia was involved (strongest evidence for that exists) yet they had connections with other random groups. I think Oswald and the Mafia did it egged on by various groups. He was connected with Russians, which is why I believe the Soviets were involved too.