The biggest problem that my wife and I had with the story is that Stone essentially skipped the parts of Alexander's life where he proved his greatness. After Phillip's death he skips straight ahead to Gaugamela, the decisive victory over Darius and the Persians. The problem is that Alexander took the throne in 336 B.C., Gaugamela came in 331. So Stone leaves out five important years which included two major battles at the Granicus River and Issus, the siege of Phoenician Tyre, Alexander's trip to the Siwah oasis. For those who aren't familiar with the history, they'll wonder just what it was that Alexander did to be recognized as great, and you don't get a sense of how brilliant he was as a general.
The other problem is that Stone focused too much on Alexander's sexuality, particularly his (probable) relationships with men, including his lifelong friend Hephaestion. The problem for me is that by focusing on that particular aspect of Alexander's life, Stone made it seem as if Alexander's sexuality was out of the ordinary, when in fact it was common in the Greek world of the time. Furthermore, in order to emphasize what was going on he made Hephaestion very feminine, which I doubt is accurate given that the guy was one of the commanders of the Companion cavalry.
Stone also has to be Stone and throw in some conspiracy theory. I suppose there has always been speculation about such things as who exactly was responsible for Phillip's death, was Hephaestion murdered, was Alexander poisoned, but the sources are ambiguous at best.
Despite all these things, I enjoyed the movie, but I think that I've given Stone a pass simply because I enjoy the subject so much. And I have to say that the battle of Gaugamela was done well, and was more or less as I had envisioned after reading various accounts of the battle. Unfortunatley, the last battle against Porus was not very accurate, although exciting.
It doesn't surprise me that the critics don't like Alexander, and I don't think it will make much money. For all the star power, I just don't see it as a commercial movie. If you aren't already a fan of Alexander and interested in seeing a story about him, I don't think it has the draw of say, The Lord of the Rings, or even National Treasure.