I suspect that some of those story lines that didn't go anywhere were setups for S2. The bridge one is, I am almost certain, going to pay off in S2, What was confusing for me was that that looked like one of the story lines from the second book so I thought that S2 might go that way but from a number of interviews, S2 is not going to resemble the second book at all.

This is complete and utter speculation on my behalf but all I could think was that Dexter could somehow become aware of Doakes' killing of suspects in questionable circumstances (to say the least!) and use that to somehow get Doakes off his back? It is mentioned in one of Dexter's VO's, in the first epsiode (I think?) of S1 that Doakes has a record of killing suspects. Just a guess, though!