I re-read this when I saw the next chapter was up - hadn't commented the first time. One thing stands out - while we read Booth's inner monologue on all the things he does because he likes her, he doesn't actually tell her that he likes her.

I know he tells her his first impressions and what he thinks of her now (all of which is highly complimentary), but he doesn't actually correct her when she says "I know you tolerate me", which seems significant in light of Brennan's response (though I might just be reading too much into it).