I have to admit I was a bit apprehensive before I saw the episode. Having the two main characters in a show become actually involved often is the harbinger of the end. Not so here!
Loved how they made a totally believable transition into coupledom while not changing their personality traits. Their interaction was still very much them and their affection and love still came through not despite their differences but because of them.
If they continue in this vein I have no doubt the show will be just as good as before.
And who wouldn't enjoy "hormonal" Bones rationally explaining crying over a corpse or Booth documenting the pregnancy by taking pictures of Bones in various resulting situations. And who wouldn't be in agreement with Angela that a picture of Booth making an omelette is more interesting than facial reconstruction, at least under the circumstances revealed:)
Admittedly, the story of the woman with retrograde amnesia was a bit of a background thing. But it also showed that pregnant or not, Bones still was the real "king of the lab".