Overall I liked it. I thought it was a bit disconcerting that they went from nothing last year to being in a full relationship, but I can deal. I'll talk meta first, then get into some specifics.
Meta was faith, both in ourselves and others.
The victim's husband has complete faith in G-d to the extent that even though his wife was murdered he believes that it was G-d's plan even if he doesn't understand it.
Sweets has complete faith in psychology so that he keeps trying to get Booth to admit that he and Brennan are having problems so that he can fix it. It also blinds him to the factt that the other doctor is not what he claims to be. (I really liked Booth figuring out exactly what was going on. It's nice to see that he does know how to follow clues.)
Finally Brennan. For a long time, she only relied on herself. Angela and Booth had both made changes in this atitude but still her first instinct is not to trust others. So, in the opening scene we see her out in the field although clearly, at this stage she should leave this kind of work to the interns, Secondly, we see Wendell dealing with a Brennan who appears to be micromanaging a bit too much. (And Wedell, I don't blame you for being more afraid of Brennan than Cam.) And finally, when Booth approaches the subject of getting a new place together, her immediate reaction is to shut it down. I think she doesn't recognize the underlying reason but I believe it's a lack of faith that the relationship will last. It takes her falling down and being unable to get back up that makes her realize that Booth will always be there for her in whatever capacity she needs him.
And let's not forget about Booth - He's insistence on splitting the cost of the house 50-50 goes back to a lack of faith in himself. He's convinced that the only way to be a good romantic partner/father is by being a traditional provider as opposed to his own dad. I'm hoping this isn't glossed over because I think his issues are as serious as Brennan's.
Other stuff.I melted every time baby Michael was on screen. That is one cute baby.
I liked how domestic Booth and Brennan already are.
The murder cases get weaker every season.
I likied that even though they were fighting, they both said I love you to the other. It means that they're in for the long haul.
Cam's hair is horrible.
So, what do all of you say?