This one's been a long time coming.
I got this question once. "Sophie, why do you like Castle when you can't stand Bones these days? I mean, they're a lot alike now."
Here's the thing. Bones started out as a show that was about ALL the characters, meaning that though Booth and Brennan were the main characters, you still got a lot of screen time and development and all that yummy stuff involved. The cases often reflected character development going on. In Boy in the Bush, you learn about Brennan being in the foster care system because it pertains to the case. She has this amazing scene where she, this woman who has a hard time connecting to people, gets this boy, and this boy gets her. You learn about Angela having a hard time staying in one place, and how much the body of this little kid bothers her, and how she feels like she's drawing death masks for people because of her job. There was some light hearted humor, but that wasn't the point of the show, nor was Booth/Brennan's relationship.
Castle, on the other hand, started out as quite a different show. It's a comedy featuring the two main characters in the cast. Sure, Ryan and Esposito and Castle's family play a part in the show, but in the end it's mostly about Castle and Beckett. The cases are portrayed as light hearted, and while they do work on solving the cases, it's not a major point of the show. Still, Castle does show moments of seriousness. In one of the episodes, a pregnant woman is suicidal and cutting herself with a knife. Instead of having Castle go in there (even though that's not the kind of thing he'd be suited for) or they could have portrayed it as this funny thing, Castle stands back and let the person who CAN deal with that do it.Beckett goes in there and acts like a professional and talks to the woman, eventually getting her to stop harming herself.
The fact is that Bones changed. Suddenly, in a big way. Booth and Brennan, and their romance, was the big focus of the show with not much time spent on individual characters. The cases all of the sudden became about the humor, the show became about the humor, and instead of having the cases having to do anything with what's actually happening in their lives, it became completely separate. The mood felt completely different. Maybe I could have enjoyed this show, it's possible (though doubtful). But really, I was focusing on thinking, "Wait, where did all of this come from? What happened? Is this a different show? Are these even the same characters?"
THAT'S where I start getting bothered. No explanation for it, nothing.
You can't do that in a show. You can't just say, "hey! I'm getting bored of this. Let's start all over again" and still have it count as the same show. This bothered me in Merlin, too, where they pretend that the first few episodes of season 1 (or hey, even ANY of season 1) happened and that season 2 was just a replay button. The fact is that it did happen.You want to hit the replay button? Here's a scenario that didn't bother me. Buffy the Vampire Slayer. Joss Whedon made the movie and then decided he didn't like the way he did it. He didn't create "Buffy the Movie 2 Sequel to Movie 1 but completely different". No, he made a TV show that he set up as completely different. That's why I can watch the movie and then watch the show without saying, "What happened?" because he portrayed them as separate, so that's how I view them.