I've been thinking about this today since I watched a lot of those History Channel documentaries this afternoon about it.
I have trouble coming up with an explanation that would justify the assassination and such a wide cover-up.
Perhaps:
1. Kennedy intended a massive overhaul of the CIA or FBI or whatever to rid it of corruption and prosecute a lot of powerful people for their abuses of power.
2. Kennedy had plans to do something that the CIA genuinely believed could lead to nuclear war and they were unable to talk him out of it.
3. Perhaps it was a plan by Richard Nixon to eventually gain the presidency. I think he had a lot of CIA and other government connections (and he had been vice president). I think in any event he had something to do with it (but didn't everyone) considering that he claimed not to remember where he was when it happened.
EDIT: 4. #3 could probably apply to LBJ also. Or perhaps LBJ and Nixon got together for mutual benefit.
EDIT #2: I think rogue's post in this thread makes a lot of sense:
http://www.tfproject.org/tfp/showthr...threadid=36705