*SPOILERS*
So from the start it's established McNulty is an asshole. A lovable asshole but still an asshole. By the end of the show its hinted that Syndnor becomes the new McNulty. Now if you watch the show back from the start and see how many times Syndnor is fustrated by his superiors, how they operate, inept partner, having his work count for nothing even though he is a natural police and one's of the morally good characters, you begin to understand why McNulty become what he is.
My favourite pick up second time around is something minor, in the scene were Haulk is watching Marlo on survellience and using a lip reader, marlo is setting-up up the fake drug pick up at the train station to mess with the police , whenever Chris (the stone cold killer) talks he is struggling to hold on his laughter. It's something so minor that you don't notice first time through but it's little touches like that that makes this show.
I also loving how the police and viewers underestimate marlo much, even though he is the most intelligent and ruthless character in the show