Patsy was never excluded as the author of the note. It looks like her handwriting and sounds like her style of speaking, right down to use of "and hence" just like in the Christmas letter, and using "and" and "hence" one after the other is a grammar error - the word "hence" should take the place of "and". How likely is it that both Patsy Ramsey and the kidnapper will be making the same error?
The Ramseys completely disregarded the instructions of the ransom note as if they were aware that calling the police and their friends and reverand over would have no impact on whether their child was decapitated or not, and even sent their other child out of the house, while supposedly under the belief that their house was being watched by the kidnappers.
There were so many familiar references in the ransom note, too many for it to have been authored by someone who did not personally know the Ramseys, specifically John.
The note was rather long and dramatic, rather than a standard ransom note, which is as succinct as possible. It was written on papaer owned by the Ramseys and with a pen owned by the Ramseys. Why would kidnappers not write it elsewhere and bring it with them, rather than sit in the home of the child they are kidnapping and compose a 3 page diatribe, risking being found out the entire time? I won't even mention again how they had the daring to molest and strangle the child in her own home, risking being found out the entire time.
The child wasn't kidnapped, which is what the ransom note specifically says this crime is about. They could have taken her and ransomed her body, if that was their intention, but it wasn't. And if they wanted to kill her, why even write such a long and blabbery ransom note? Why kill JonBenet and not Burke? I guarantee you a foreign faction would have been more interested in killing/kidnapping the son than the daughter.
John and Patsy have both changed their stories about the events of Dec. 25th - 26th. They have outright lied and tried to resist assisting in the investigation. They tried to flee Boulder as soon as their child was found dead. They refused to go in to be interviewed for months on end.
They sent Burke back to school right away, seemingly unconcerned that there might be a killer targeting them.
I'm sure I'm forgetting things, it's late, but all of these things together, logic and evidence, point at one of the Ranseys being the perp and not an intruder at all.