I've always believed John Andrew needed a much closer look and questioning. My initial reaction was: The adult brother did it ( he's a half brother).
He had means and opportunity, and the psychopathology is likely tied into his sister's, Beth's death a few years earlier, which devastated John so badly he kept portraits of her up all in the Boulder house rooms he frequented.
Motive: Hurting " Dad" more seriously by taking away the child he loved most in the world with Beth gone, get back at the stepmother he may not have accepted or loved ( we don't know the family dynamics because they come from the Paugh narratives and the Paughs were ALL disordered in their thinking about a molested and murdered 6 year old granddaughter or niece.)
Is there a true sexual motivation to the crime? Yes, in that she was penetrated by an unyielding object and parts of Patsy's paintbrush fibers were found in JonBenet's vagina. But, no semen was recovered as far as we know from the body.
I don't think the presence of a comforter containing John Andrew's semen plus a very young child's book is BENIGN. I think it has great meaning, and likely had been used before and left in the basement. There's little doubt as to who used it, but what we don't know is if any fibers from JBR's clothing, nightclothing, or urine or other DNA from JBR was recovered.
Most of the descriptions say the semen was " old" but I'm not sure what determines old or new except sperm motility under a lab slide.
John Andrew returned to Atlanta at some point during the Christmas time, but his presence was " confirmed" by a man with a hoodie on in dim light using his ATM card. What I'd like to point out is that I lived in Atlanta at that time, and it was COMMON for young males to give their friends alibis using the " hoodie at the ATM" or gas station defense. It only takes one friend who looked like him and had one of his bank cards, or even one of his parent's bank cards he was authorized to use. We do not know if he was an authorized user of a card his mom, Lucinda, had, but I'd think it's likely. So, IMO, it's not a confirmed sighing of JAR. It's a confirmed sighting of a tall white young adult in a generic colored hoodie at night.
I believe Patsy had strong suspicions that someone in the household was committing a juvenile type of sexual assault upon JonBenet chronically. Digital penetration vs. penile penetration, but not from a small 9 year old according to the measurements in the autopsy report. It is likely, from the vaginal opening measurements, that she was being groomed for penile assault. A 6 year old has a tiny body. This was a determined person who was also a patient and gentle person.
There are other reasons I hold close because of things known, seen, heard and witnessed after the Ramsey family returned to Georgia after JBR's funeral to think a grown male in her family was the abuser, thus, likely the person who killed her.
Reason for murder? She had gotten old enough and verbal enough to tell things about what was happening. Plus, anyone else remember her huge number of visits to the Pediatrician in the year before her death? Patsy knew something was wrong, Dr. Beuf knew something was wrong for a 6 year old to have recurrent vaginal infections without the usual prepubescent flora and lack of estrogenic factors which protect a little girl from yeast infections.
Irritation from bubble bath is external. A yeast infection is internal and should be a red flag alert to a doctor, and likely was.
We know the GJ in Boulder had returned a true bill of indictment against Patsy and John related to the murder. The ONE piece of evidence I've always wanted to know and see is the testimony from Fleet White and Priscilla White, the last 2 adults to see JBR alive outside her family. I hope Fleet's still alive and doing well, as he may be the key to unlocking the truth, or his wife and children in the case of his demise.
All of the above is IMO, only. It is speculation based on circumstantial evidence plus direct evidence at the crimescene which has been released to the public over the past 20 years or so.
I believe there WAS someone else inside the house, someone who didn't belong there that night, but I do not believe he was a stranger intruder at all. One day, John will die, and we'll know what happened, because his surviving children who are innocent will talk and one will be left standing alone- the perpetrator. I truly believe it was a murder within JBR's extended family.
Whatever we believe, whether intruder or family, or deceased family, we can't bring an innocent and beautiful little girl back, a child who likely would have had an extraordinary life except for a violent murderer and pedophile who walked freely in her space for years.