Not only doesn't the Warren Commission report make sense but the government came up with two there contradictory versions. The House Select Committee report comes to different conclusions and the most credible version, or at least partial version, is the Clay Shaw trial which provided a lot of evidence that is hard to dispute. It has been demonized but not debunked in a rational manner; although there are problems. the biggest problems seem to be a result of the stone walling by the federal government.
I went into more detail in my o=wn review if you're interested.
http://open.salon.com/blog/zacherydtaylor/2011/06/13/jfk_and_the_unspeakable_james_douglass