Stone definitely believes there was a conspiracy, even while acknowledging in the notes included in the book portion of the director's cut of the film that it is possible there was none. Where he opened himself up to criticism is that he did not pick a single hypothesis and go with that. While the movie is centered around the alleged involvement of Clay Shaw, Stone basically threw out all the various possibilities that have been put forth over the years from Cuba to the mob, to the CIA orchestrating the hit. He couches the various hypotheses in the story by using words like possibly, maybe, etc, to describe what could have happened. Stone does a great job weaving in old news and archived footage with scenes that he filmed. So much so that it was hard to tell at times where the real-life footage ended and the movie started. Stone's stated intention however was to provide all of the "theories" that are out there, and let the viewers make up their own minds. To that end, regardless of whether you believe that was the responsible way to approach the film, it succeeds. Another way Stone leaves himself open to what is probably the most valid criticism is that he included material that was just plain inaccurate. The big one that comes to mind is the trial scene recreating the magic bullet when he placed Kennedy and Connelly directly in line with each other on the same level. In reality, Connelly's seat sat lower and off-center, which when taken into account omits all the turns that the bullet would have to do in the whole "left, then right" sequence of the film, which was one of the most powerful sequences in the movie.
The lynchpin of the film's quality, regardless of whether you agree with the substance, was the acting. Many A or B list actors who were alive at the time had a role in the film. Some little more than cameos, but it really was a who's who when it came to the cast. I think Costner did a great job making Jim Garrison much more of a heroic figure than he really was. Garrison's overall reputation outside the JFK case was pretty checkered. The film boasts a cast that includes Donald Sutherland, Sissy Spacek, Walter Matthau, John Candy, Tommy Lee Jones, Gary Oldman, and Kevin Bacon, among many others. There was not one bad performance in the bunch.
I am not sure how long the theatrical version of the movie is. If memory serves, it was just under three hours. This clocks in at just under three and a half hours, with a lot of additional and extended scenes. Including a 5 minute or so narrative at the beginning of the movie that describes Kennedy's presidency up to that point. There are also a few features included as extras along with even more deleted scenes. Chances are anyone reading this by now already has a strong opinion of the movie. For those who do not, as I said regardless of your position on whether there was a conspiracy or not, you can still enjoy the acting and the non-fictionalized historical aspects of the movie. If nothing else this will always be a movie that is a conversation starter and a thought piece.