I had a sudden thought.
In general, while I feel this episode was much, much better than the last few, it still is missing the old zing.
One thing did occur to me. Obviously, the theme of the episode was honesty. Note that the episode did not come down on the side of honesty always being the best policy. But it did come down on honesty being a necessity in a relationship - look at Angel and Hodgins. Both of them were keeping things from the other and it was becoming detremental.
Now look at Booth and Brennan. He is not being honest with her. When she asked him to tell her something he had lied about, he basically skirted the entire issue by instead talking about a lie of omission which was basically meaningless. All he really said was that he was glad that she was there for him during a tough time. Until he learns to be more upfront, this relationship is going no where.
(and if they keep stalling, this show is going to continue to fall apart.)