Ten years ago I had the honor of attending a Mayo Clinic Lecture. The speaker was Dr. Ivanov, who did the DNA testing on the Romanov remains. His presentation, with the DNA results up on the screen as he talked, left no doubt in my mind, as much as I wanted to believe that someone escaped from that cellar, that the Tsar Family (as he referred to them) had all died on that July night.
As for Maria and Alexis not being found in the grave, a possible explaination is that Maria's body was mistaken for Alexandra's body and disposed along with Alexis's as such. Maria was tall, like the Empress, and had a sturdier build than her older sisters. The famous "note" outlining the murder and burial of the Romanovs contains the information that the Empress's body and Alexis's body were both burned, not buried with the rest. Since we know Alexandra was identified by her exquisite dental work as well as her DNA after being found in the burial pit, and the youngest female skeleton found had the skeletal characteristics of a female about Anastasia's age, not older like Maria, the scientific evidence seems pretty clear.