Oh boy. This is a complicated issue, and I don't claim to be anything even close to the foremost expert on this but I will try to at least address this as best I can, seeing that no one else has. But bear in mind that some of this is speculation on my part, based on observations and things I read, rather than expertise and first hand knowledge, so I could be wrong about a lot of this.
Yes, it does seem that Shark and his team were doing a lot of the work that you might normally find the police doing. But one thing you have to consider is that Stark's team works for a Fictional unit, the High Profile Crimes Unit. So obviously, it's hard to make an accurate analysis because since the unit is fictional, the powers, resources and jusridiction of the unit is speculative.
In reality, the DA's office does have it's own investigators, like Isaac. And I believe that some of these investigators do work exclusively for specific units of the DA's office. And from what I can tell, it does seem like Isaac's duties are pretty realitic in general, namely, to provide investigatiove support to the DA's office (my understanding/assumption is that once the suspect is charged with a crime, the DA's office is now in charge and while they may work with the police further, in many if not most cases, they would probably be using their own investigators for most of the work unless there are specific police units much better equipt or designed to handle the cases even after arrests have been made and charges filed).
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Now, I believe that you are referring to episode 4 of season 2 when you talk about the battle for control with the FBI. I don't know how clearly you remember the details, but in the episode, as soon as they determined that the bombing was not a terrorist act, the FBI closed their investigation and the jurisdiction went to the State, in this case, to the Los Angeles DA's office. If you are wondering about why it would go to the DA and not the police, I can only speculate it was because the FBI did not close their investigation until the suspect was identified and arrested, so the police were no longer needed to investigate.
Jurisdiction itself is a complicated issue. Normally I believe when there is a question of exactly who has jurisdiction, it really seems to get handled by the higher ups of whatever agencies are involved - therefore, you normally see the federal agencies win over local agencies because they tend to have more clout. Obviously, as in the example above, once facts are discovered that weigh in favor of one agency or another, the lead of an investigation can change or some agencies might withdraw their investigations entirely. I highly suspect that in reality, there are fewer battles over jurisdiction between agencies than TV might lead one to beleive, since in reality the evidence in most cases probably point to whom should retain jusrisdiction a lot more clearly than what you see on TV. Plus, I would think (and hope) that interagency cooperation is more common as well, since no agency is going to want to tick off other agencies any more than completely necessary, because they know it can turn around to bite them in the rear some time later. That's pure speculation on my part, of course, but I doubt you have as many hot headed loose cannon types in somewhat high positions like Stark or Gibbs in real life.
As for other aspects of the show, well, I won't go into great detail about all my opinions but I will say a few things. I understand what you mean about going into the lives of the other chracters a bit more, and I think had the show survived a few more seasons, it would have been much more important, but after all, the show really only had a season and a half. And what with some of the characters killed or written off, and not knowing the exact reasons/circumstances behind those, I can kind of understand that maybe the writers wanted to focus more on Stark and his immediate surroundings because god knows if James Woods was going anywhere, they wren;t going to have a show anyway. As far as Madeline and Casey went, well, maybe they would have gone more into that had Casey not been written off, but on the other hand, thw two weren't having a real relationship, it was just sex (which was stated I believe by Madeline). as for Martin, well, I didn't dislike the character by any means but I have to say that usually you do not spend much time on a character who has been killed off, especially not one that didn't even last the first season. Normally when a character like that is killed off so early in a show, the show tries to move on quickly without them and regardless of whether I liked the character or not, I think that was the smartest thing to do once the decision was made to kill off the character.
I also think if you go back and rewatch the show, you'll realize that Casey's dad wasn't talked about all that much - he was more of a plot device than anything else. Maybe had Sam Page stuck around for more, they might have done something, but since he didn't, it's probably best they didn't spend any time on it.
The one thing I really disliked about the show was the way they handled Julie. Okay, I'm fine with the whole "I'm not the perfect faughter you want me to be" thing, but honestly, from the pilot they make her appear to be wise beyond her years, they later talk about what a good student she is, and yet they continue to put her in situation after situation where she makes a lot of really stupid choices. It was irritating that not only were they completly inconsistant about that but also the teenager angst theme was just way too cliched, especially since the rest of the show was reasonably smart and well written.
I also didn't much care for Raina Troy. She, too, was a bit too much of a walking cliche, but worse than that, she was, like Julie, not written consistantly. Originally described as a brilliant but a contempt citation waiting to happen, yet she never really did anything briliant and the only person she actually ever seemed to get inthe face of was Stark, and maybe Madeline inthe early episodes. Worse yet, she seemed to not get the reasons why they had to consider Isaac as a prime suspect in his dead fiancee's investigation when they re-opened it. Any even halfway decent DDA would have known that you have to look at all suspects on a case, and surely someone who was supposed to be brilliant would have realized that 1) the sooner you clear Isaac, the sooner you can move all of your resources off of him and 2) you would want to not only investigte Isaac, but investigate him thoroughly because since as Danny pointed out, the fiancee is always the first suspect, you make damn sure that there is nothing that the defense can use against isaac that would give their client reasonable doubt. Not only is that obvious, but it's something the HPCU has dealt with before. And yet she handled that situation like a complete rookie.
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