The suspect maybe maybe had a dual motive, like a grudge against the Ramsey Family, but his motive there was sexual pleasure, he only killed her, either by accident to keep her quiet, or on purpose to keep her quiet. But, yeah, the whole thing was sexually motivated. What kind of disciplined kidnapper would do all that shyt in the basement? The note was probably to confuse, while he abused her somewhere. Also, some of the things he brought with him, including maybe a stun gun, but the rest he improvised, including the paintbrush thing. And the ransom note.
My best guess is this is someone in the neighborhood, who has been in the house before. Maybe a service person, but my thinking would be more like the loser son of one of those families. Mid 20's, under employed. 18-25. Maybe older. What now is kinda called an incel. Someone who had been in the house for parties/block parties, gatherings of some kind, and knew something of the layout. Someone who became obsessed with Jon Benet and came up with a plan to act on it.
A lot of times suspects like this leave afterward, their 'post offense behavior' gives them away, heavy drinking, trying to insert themselves in the case, and they often leave, if they are able to, so maybe a return to college, or a transfer of schools, or a move out of state. Police let this person slip away by fixating on the Ramseys.
They weren't from out of town, it wasn't random, it wasn't a kidnapping for ransom. Someone saw that 118,000 on a piece of paper while creeping in the house, that day or before. It's like the Idaho murder. You don't just randomly break into a house and go door to door, he knew exactly what house, and what people were inside, because he planned it out.
The ransom note is by far the most exculpatory piece of evidence. The Ramseys didn't write that weird shyt, under pressure in the middle of the night.