The bogus note implicates Patsy and the lack of a realistic point of entry seems to exclude anyone outside the house unless they had a key. The police video of the window from that morning has me convinced no one came in through that window, but who outside the Ramsey family would have a key who hasn't been investigated?
Overall, it's the sheer implausibility of everything this intruder must have done that gets me. Talk about an idiot savant. He commits the crime of the century without leaving a trace besides one of six highly degraded incomplete touch DNA samples on her clothing, gets in and out like a ghost...but does every convoluted unnecessary thing he can think of during the hours spent in the house. After loosely binding her, putting tape over her mouth and stun gunning her he feeds his victim pineapple from a bowl that somehow already has her brother and mother's fingerprints on it. He sits down to read their bible and circle a certain passage and moves some Kleenex boxes and whatever else the Ramseys accused him of messing with. Like the flashlight: he takes it from the drawer in the hall where it was kept and moves it a few feet over to the kitchen table, wiping it for prints inside and outside (because he had to remove the batteries with his bare hands that night?) - except wasn't most of his crime committed in the dark basement anyway? If you believe Patsy's initial statement that she changed JB into her red turtleneck before bed, he must have changed her back into the shirt she wore to the Whites' and left the old one on the bathroom sink. Of course Patsy changed her story later. When does he leave his entirely useless ransom note on the spiral stairs? Not before he abducts JB from her bed. He would have to hop over it in the middle of the night holding a child. The police questioned if Patsy could hop over the note unencumbered in daylight! If he did it after killing JB, does that mean he murdered her in the basement, ran upstairs to place the note, then went back down to the basement to climb out the window (without disturbing any spiderwebs)? And for that matter, we know he replaced her underwear. Did he grab a pair of underwear from her drawer, hide the rest of the package somewhere in the house for some reason, then abduct JB? Or does he get down the basement, murder her, decide he wants to clean her up and replace her underwear, and run back upstairs to find a pair. At some point he stops to get JB's blanket out of the dryer. Why bother to do any of that? I could expound on this subject for days but you get the picture.
And then there's the issue of motive. We have a kidnapper who doesn't kidnap but does murder and molest. He leaves a ransom note threatening to withhold her body for "proper burial" and then leaves her body in the basement! Never tries to collect and barely asked for anything anyway. We have a murderous pedophile who gets his jollies with a paintbrush (seriously?) and cares for the victim after she dies, cleaning and redressing her and wrapping her up in a blanket to look like she's sleeping when she's found. And we have a murderer who murders twice: first with a blow to the head and then when that didn't finish her off (or produce any visible damage) he takes the time to seek out materials to stage a bizarre, amateurish & highly visible secondary mode of death with the "garrote" instead of just bopping her on the head again and getting it over with. If a kidnapping gone wrong scenario, she had to have died accidentally, and you don't get garroted accidentally, so why take the time to throw that in? If it's a pedophile, why do both when either one would be sufficient? And if it's a pedophile, why go through the elaborate kidnapping ruse? Strangers don't stage, people close to the victim stage to deflect attention. And that has been the Ramseys' MO since day one: deflect, distance themselves, obfuscate.