Yes, such a mystery... I have heard that the remains that are reburied in Mary's grave may in fact not even be her. It is possible, after all in '45 the Russians opened the grave, and from what I have heard paying little respect to the dead, or giving any notice of who lay in the grave, and so it could be possible the wrong remains were buried. Again in the 90's her grave was opened and the remains stolen. It was said that the remains were taken back, but again it could be that the wrong remains were reburied.
I do not know what to believe, perhaps Rudolf killed Mary and himself - I think that happened - but I do not believe it was the romantic tragedy we have been told. He may have cared for her and longed for her as he has other mistresses, she may have adored him as a teenager adores her idol, but I do not believe it was the true tragic love. Rudolf just didn't want to die alone, No matter how romantic and dramatic the movies are, almost all they depict tragic love, it is not sure if that is the truth.
But then again, it was at first said that Rudolf and Mary died in short time of each other, but there were several hours between their death, and also I am wondering too why the Empress was not allowed to see the hands of her son, or to why all evidence has been destroyed - Ofcourse the Emperor may have wanted to keep to the original story of heart failure, thus destroying all evidence of Mary's death at Mayerling. Also her mother was forbidden to speak of the events, so it is possible the Emperor simply didn't want it to be known - and also I would love Rudolf's remains to be examined, and those that lay in Mary's grave - so they can perhaps be identified as Mary, but for now it all remains a mystery.
I recently received a copy of the movie 'Le Secret De Mayering', which is in French, retelling the story of Rudolf and Mary as a romance indeed but not as the tragic, doomed love, as it always is shown. This movie states that the couple was assassinated - we can see a gun pointed at them, but do not see them being shot, though someone escapes the room by the open window after their death - and uses several sources, Countess Larich's book for one - now that is mostly credited as a book full of lies, but this movie also shows that conspiracies always will be believed until the truth is completely out in the open. I have posted screens and more on this movie in the thread about movies on Sisi.