The placement of the flashback was a small thing, but worked really well for me here.  Not only is it not at the beginning, where it would have ruined the Shawn-attached-to-a-Polygraph tension, but it's also right next to Lassiter on the polygraph, when we see him use the same techniques Spencer Sr. is teaching Shawn…

Honestly, I think Roday being annoying works better in this show than similar smug-always-right-quipsters work in other shows, because when he's at his worst, the other characters in the show are irritated by him too.  If nothing else, it's a nice reassurance that his character is intentionally over the top, rather…