Everything we post is only our opinion, as no one here (that we are aware of) knows the truth. If there were solid proof, we wouldn't need to be here, because the case would be solved. That is why it is NOT solved- because there is no solid proof. In the absence of that proof, obviously people have varying opinions on who the perp(s) are.
There are so many pieces of this puzzle, and many of them fit, but many do not, that in the absence of solid proof, it seems like solving it is hopeless.
There is a lot of information on this case that you would find helpful, and there are sites that have the information all in one place. It is difficult to get a good overview from the forum sites. I found watching the DVD of "Perfect Murder, Perfect Town" was helpful at the beginning, and I also read the book.
That being said- a ransom note was left. Kids that hide in a freezer or fridge don't write ransom notes, especially one like that (I assume you have read it, it is available online). It is very suspicious that the father of a supposedly "kidnapped" child goes straight to a hidden basement room and "finds" her. Why wouldn't you check her room first? The detective told him to see if any of her things (clothes, toys) were missing and he goes to a hidden basement storage room first? That, to me, is suspicious.
Whenever a "missing" child turns out not to be missing, but found dead in her own home, the parents are always the first suspects. JB's parents were home when she was killed, and that makes them suspects for that reason as well. The FBI were on the scene at the very beginning, knowing nothing about JB or her family, and they told the police right away "you're going to be finding her body". They knew right away it was no kidnapping. They were right.