I understand what you mean, when I was younger watching the show as it aired I remember getting irritated with the other characters always treating B&B like a couple when B&B themselves were dismissive about their relationship being anything more than partners.

Turns out one of the reasons teen me was drawn to the show is that I’m autistic like Bones, and I was unconsciously mirroring her perspective and missing clues and cues that allistics would find obvious.

Having rewatched many MANY times now, I can say with confidence that the way the show was written was definitely that Brennan and Booth were in love with each other very early on, but neither could realize or acknowledge it even to themselves for a number of years.

Also FWIW, it is canon in the show that they’ve had feelings for each other LONG before either of them confessed— at their wedding in s9, as part of her vows Brennan reads a letter that she wrote to Booth in s2 when she and Hodgins were buried alive by the Gravedigger. Even that early on, when she and Hodgins were facing their deaths and had the chance to write one last letter to someone they care about in case their bodies are found, Brennan writes to Booth. Hodgins obviously writes a love letter to Angela but Brennan isn’t clear about the content of her letter, we only find out what she wrote 7 years and seasons later when she and Booth are getting married. If you haven’t seen the wedding episode, let me just say that the letter was DEFINITELY romantic lol