People complain that the movie fails to show why Alexander was considered great by his men. I think it does make this clear. His men consider him great because together they have founded cities and conquered Egypt, Persia and more. Alexander has fought these battles with them and shared in their failures and successes.
Also people complain that the portrayal of Alexander is ? All I can say to this is that America is used to the typical movie hero: Someone like Maximus in Gladiator in whom we don't see any internal conflicts, but whose internal resolve overcomes the immense external obstacles he faces. Oliver Stone portrays Alexaner as human. The media and the American public would have liked him to copy Gladiator and tell the story of how a man's internal will and resolve overcomes countless conflicts he faced. Instead Stone shows an internally conflicted man, whose total devotion to a vision drives him to greatness.
As for the relationship between Hephaistion and Alexander, the movie shows EXACTLY what we know from the historical writings of Arrian and Curtius. Alexander felt closer to Hephaistion than to anyone else in his life, and homosexuality was a part of Greek/Mecadonian society. The movie never shows Alexander actually engaging in homosexuality, and, just like the historical facts, you can interpret it however you want to.
I admire how the movie stayed as true to history as possible. But most of all, I admire it for what most critics criticize the most. The movie doesn't pick one central conflict and develop it to its resolution, but instead shows how Alexander puts the pursuit of his vision above all other conflicts in his life. As Ptolemy says in the ending speech, it is the pursuit of our visions that leads a man to greatness. Stone's Alexander shows this and I believe Alexander should be considered a great film as well as a great leader.