The 'Fly in the ointment' for me will always be wound morphology.
Governor Connelly's wounds were consistent with a thick jacketed bullet that would pass through a human target with minimal deformation. (Like the one that was recovered)
President Kennedy's wound was not.
I'm not a conspiracy nut and I don't have any alternative explanation at all.
--But at the same time, I dislike loose ends and the attempts I've seen to explain this have generally been laughable.
For example, "Experts" have compared the 6.5X52 with a 30-30 because both catridges propel bullets of comparable weight at comparable velocities. The idea is that it would not be entirely impossible for the bullet propelled from Oswald's rifle to have done what we can clearly see in the Zapruder film. (These comparisons are usually based upon photos in the book, Gunshot Wounds: Practical Aspects of Firearms, Ballistics, and Forensic Techniques. DiMaio, Vincent J.M.: Elsevier Science Publishing Co., Inc., New York, NY; 1985)
-- Problem is the 30-30 is a hunting cartridge, not a military cartridge and as such it is loaded with soft-nosed bullets 99.9% of the time. (Full jacketed bullets in most 30-30's are dangerous because of the tubular magazines.) This not only invalidates the comparison, it lends weight to the idea that the wound was not inflicted by the bullet in question.