The wonderful irony of Brennan and Booth is that out of all the characters on the show, Brennan is the one who eschews marriage the most and, out of all the characters on the show, Brennan is the one who needs--and thrives on--a long-term, committed, stable romantic relationship the most.
The second wonderful irony of Brennan and Booth is that like so many women throughout history, Brennan's long-term, committed, stable, romantic (even if she doesn't know it yet) relationship is with a man who is the mirror of her father.
And this isn't even me. This is the writers.
The writers go out of their way to pinpoint similarities between Booth and Max Keenan. Booth understands Max Keenan's philosophy ("Law of the Jungle") and defends it to Brennan. Booth encourages Brennan to support her father, especially after Booth arrests him. Max himself selects Booth as his back-up ("You take care of her"), and I have personally always been convinced that Max kills the Deputy Director as much for Booth's sake as for Brennan's. Speaking of that particular episode--"Judas on a Pole"--the writers/directors make a deliberate visual connection between Max and Booth when they morph from Max watching the body burn to Booth watching the burnt body: same pose, same stance.
Booth is Max's anti- or mirror. He isn't a clone. He is the good guy (who occasionally, unknown to Brennan, protects her by jungle means); he is law to Max's disorder. I love the scene in Season 3 when Booth says, "I'm good. You know back in the day when people were dumping tea in the harbor, I would have rounded them all up. We'd still be British."
And Brennan laughs. Brennan needs a man with a consistent worldview. She also needs a man who won't end up getting her killed because of his "outlaw" tendencies. She needs, however much she intellectually dismisses the need, the "knight in shining FBI standard-issue body armor," as Angela puts it. And she's got it: she's got the guy who, unlike her father, won't abandon her but, like her father, will protect her.
And she protects him. I'm not a big advocate of needy people hooking up on the hope that they will solve each other's needs. I am a big advocate of people complementing (and complimenting) each other. Two people with similar neediness: BAD. Two people with complementing neediness: GOOD.
Brennan needs stability. Booth needs someone to protect. He is pure Alpha male, tempered by self-doubt. Booth was a sniper--and a good one. He doesn't have a philosophical or legal or moral problem with being a sniper or with shooting bad guys. But he doesn't want to do it anymore. It isn't about Booth saying, "Oh, I was a horrible person." It's about Booth saying, "I no longer want to take on that particular function." He wants a constructive role rather than a destructive role. This is, bluntly, Alpha male patriarchy at its best. (Yes, it does exist.)
Booth doesn't want someone to domineer and wouldn't tolerate that kind of relationship for two seconds (good Alpha males rarely do). Rather, he wants to play a constructive role in someone's life--someone who needs him.
Clark Kent and Wonder Woman: hey, it could work!