What would have been the motive? Why would a doting mother kill her daughter?
Perhaps Mother walked in on JonBenet and someone else in a sexual act and went into an uncontrolled rage that resulted in a fatal injury to the child. I am not judging, so this is pure speculation - but would explain the 'staging' of the body, the change in pajamas, and many other anomolies.
quote from Vanity Fair:
"...Dr. Richard Krugman, a specialist in child abuse brought in as a consultant by Hunter's office says that there was a vaginal abrasion, which is a sign of trauma(but), it is not a sign of sexual abuse, necessarily"
"Dr. Cyril Wech, a wellknown forensic pathologist, has no doubt that the 45-pound child was molested. "If she had been taken to a hospital emergency room, and doctors has seen the genital evidence, her father would have been arrested."
"The vaginal opening, according to Dr. Robert Kirschner of the University of Chicago's pathology department, was twice the normal size for six-year-olds."