I finally figured it out: the writer in charge of Danny Messer's and Lindsay Monroe's storyline is a fanfic writer. Danny's life on the show is one big hurt/comfort angst fest and Lindsay is the improbable Mary Sue who comes to save him.
Danny is a tough cop with an attitude. In season one he's tied to some new school mobsters who call themselves the Tanglewood Boys. He is also involved in a shootout that results in the death of an undercover cop. For the entire episode Danny and most of the cops think he killed the guy. He didn't, but it was still a bad shoot because he was shooting wild on a crowded subway platform. Danny doesn't help himself any by talking to IAB when Mac and everyone else he knows tell him not to. At the end of this affair Mac tells Danny that he was strongly cautioned against hiring Danny and if he did, one day Mac would realise that he made a mistake. Mac says he finally realised that he had.
In season two Danny's good friend Aiden gets fired and replaced by Mary Sue. We find out that Danny doesn't get along with his brother Louie too well. Danny also gets connected to a murder performed by the Tanglewood Boys that had happened 15 years earlier. The events of that night 15 years earlier were also what damaged the relationship with his brother. Louie had intentionally made Danny angry and storm off because he knew the other guys would murder the victim in question and Louie didn't want Danny to be a part of it. To exonerate his brother, Louie gets the main Tanglewood Boy to confess on tape about that night. Louie then receives a fatal beating and dies. Two weeks later Aiden's burnt up body shows up in a car. She was killed trying to catch a serial rapist.
Later on Danny feels responsible for the death of his neighbor's kid because Danny had taken the kid to a Bodega and they ended up in the middle of a robbery where the kid is shot and killed. He sabotages his then current relationship with Lindsay to have guilt/mourning sex with the kid's mother. The affair runs hot and heavy but then she gets her head together and moves away. He goes back to Lindsay. The next season Lindsay tells him that she's pregnant. Lindsay says that she knows him and doesn't expect anything from him. He doesn't take it too well, but then decides to step up. When he offers to marry her, she rejects him.
Then there's a lot of angst about the baby and the relationship but they eventually end up married. And then Danny is shot and paralyzed. Danny learns to walk again. The crazed murderer who had fixated on Danny three seasons prior follows the family on vacation, attempts to kidnap the baby and ends up getting shot by Mary Sue, er Lindsay.
Then you get to the actual relationship between Danny and Lindsay. These two characters work together, start dating, are known to be dating by the other characters, get pregnant, get married, and are STILL working together. I'm sure that happens in other jobs and on other shows and it's not weird. For CSI: NY? It's weird. And it goes against what's been established in the show universe. On CSI when the relationship between Grissom and Sidle is revealed there's heavy criticism and Sidle has to change shifts because if they're dating they can't work together. When Hodges was trying to get a date with Wendy, Catherine Willows cautioned him that if they did get together one of them would have to change shifts. On CSI:NY when Flack was seeing Angell and their relationship came to light during an IAB investigation, there were a lot of concerns about the effect it had on their professional relationship. And Flack and Angell weren't partners and almost never worked a case together (unless it was convenient for the writer as a way to move their story along -_-). Meanwhile Danny and Lindsay get a pass?
Lindsay Monroe is a Mary Sue. That's the only explanation.