O.K., as I said above, I'm way late to this, and not informed other than the basic facts. It appears many on this thread believe a Ramsey family member murdered this child and in the most heinous of manner. Why? It's somewhat easier to understand uncontrollable rage and an impulsive action that resulted in death. But the garrot, molestation, etc? So depraved. Was there any signs of that type of depravity in this family previous to this murder? I have vague memories of Patsy Ramsey's inverviews. She always seemed heavily medicated to me, but who could blame her really? I think she would have been easy for the general public to dislike. She was privelaged, and had an affected communication style if I remember correctly. She just seemed like she was living through her kid.
Yes, most people here are RDI (Ramsey Did It) with subcategories of JDI/PDI/BDI or any combination. Few here believe an intruder did it (IDI)
IDI has more going for it than most here will admit. As you point out, there were no prior signs of depravity. (The autopsy did reveal prior sexual abuse consistent with digital penetration, so even though there were no signs of this, it must be acknowledged as having happened)
The garrotting seems extreme and it's understandable that many wonder how a parent could do this.
There were unsourced white and brown fibers at the crime scene.
The crime scene was badly managed, and badly contaminated. So those who claim the intruder left no trace of himself may simply be wrong.
Most RDIs think the touch DNA didn't have to belong to the killer. And they are right, it didn't have to. Most think that the existence of 6 examples of artifact Touch DNA, something Kolar reveals in his book, make the TDNA even less likely to be from an intruder. They take the stance that all the TDNA must be intruder dna, or none of it is. IMO this is logically wrong. While it's certainly true that none of the TDNA has to belong to an intruder, it's not true that it has to be all or nothing. One artifact TDNA sample could be from the intruder, while the others are not. For a jury, there are now six pieces of evidence for an intruder, not just one.
So, why am I, and most others here RDI if the intruder theory is that strong?
1. I do not find it plausible that an intruder would write what is apparently a ransom note, then leave the body behind.
2. Nor do I find it plausible that a sexual killer would leave a note of any kind.
3. The crime morphs from kidnapping to sex killing. This seems unlikely to me; even if the kidnapper were a pedophile he could wait and get his jollies back at the hideout.
4. The crime scene looks neither like a kidnapping, nor a sex killing. As soon as the body is found we know there was never a kidnapping (except in a technical sense in which Cynic has shown JR might be charged with felony murder) the body is there, so obviously, the kidnappers didn't take her. There is no sign of a sex murder until the body is unwrapped on the autopsy table. If it were an intruder, the crime would look either like a kidnapping, or a sex murder. It doesn't even look like a combination of the two. It looks like she was murdered in her home and her body hidden in the most remote room in the house.
5. A kidnapper abandoning his plan would have to have a reason for abandoning the plan. Since he'd already got JB out of her bed, down to the first floor, and down to the basement, why not just complete the kidnapping? And why go down the basement? And if he did abandon the kidnap plan, why wrap the body in a blanket and hide it? He'd just get out of the house at that point, leaving the body on the floor. And how to account for sexual abuse if it's a kidnapping?
6. If it was a sex killer, why the RN? And why does he re-dress JB, then wrap her in a blanky, then hide her in the WC? He'd just leave her where she lay, and leave the house.
7. The basement window was not a point of entry that night. There was a grate over the window well (why would the intruder stop and put it back after making his exit?) there was a spider web attached to the grate, so obviously it was never removed, and the dirt on the window sill was not disturbed enough to indicate someone slid his butt or belly across it, as would be required to get in.
8. I'm confident JR lied about breaking the window earlier in July or August. It doesn't ring true, and if there really were an intruder, he'd wouldn't have had to make up this story.
9. The amount of ransom asked for is too small to be a real kidnapping. It looks to me more like the amount JR can lay his hands on very quickly, and is willing to kiss goodbye than the amount a kidnapper would ask for.
10. An intruder scenario does not explain the evidence of chronic sexual abuse, consistent with digital penetration; not unless the intruder had visited several times, or had previous access to JBR.
11. The work Whaleshark has done, magnifying the handwriting of the RN, shows two things - One, the original hand was disguised by the addition of lines, squiggles, and in some cases writing over the letters again. Two, much of the original hand appears to be JR's. Whaleshark also believes some writing looks like PRs. So, if it were an intruder, how in the world does he manage to mimic JR's writing, then mimic PR's as he disguises JR's?
In the end, the intruder theory isn't plausible, despite having a lot going for it on a superficial level.
Sorry, didn't have time to edit. I could have combined a couple of those, but you get the idea.