OK, to put my opinion to rest I think that while Bubastis an important little detail that adds a bit of humanity to Adrian in the end despite the atrocities he committed, I think that Bubastis may have made a little more sense if she had appeared a bit earlier in the film rather than just out of nowhere and only getting a few minutes of screen time before dying. The problem I had with her inclusion has really nothing to do with the squid not being there. I agree that her purpose is several things: to at once make Adrian seem that much more exotic and wierd but also add some humanity to him because he actually cares about her, showing that he at least gives a damn about life of some sort. Also, her randomness is crucial because its like a sort of Citizen Kane deep focus trick.
Anyone who has seen Citizen Kane remembers the flashback scene where Kane's parents are talking to the man who is informing them of his massive inheritance and need to come with them, all the while in the background through the cabin window we see young Kane playing on his sled in the snow. Most people I know who have seen the film can't remember much of anything that the adults were saying because due to the deep focus, you see a completely visible in focus boy playing around and it's all you can pay attention to. The same kind of trick was used in the graphic novel when Adrian is in his tropical rainforest greenhouse explaining his whole outlook on life in great philosophical detail to his henchmen. During this whole monologue, Bubastis is running around playing in the greenhouse. I don't know about the rest of you, but I had a hard time focusing on readin Adrian's monologue because in another sort of deep focus trick, all I could really pay attention to was Bubastis running around the greenhouse chasing frogs and whatnot.
However, I feel that if she had been given a couple of more brief appearances throughout the film her death and her purpose of giving a bit of humanity to Adrian might have made more sense. Even just brief glimpses of them together more than just at the end would have made the whole inclusion of Bubastis a bit more logical and impactful. However, I had no real problem with her inclusion, I just felt that she wasn't properly used to give her death a real sense of pain.
Your post makes sense until the Christopher Nolan part. What on earth does Christopher Nolan have to do with this discussion? I take it you didn't like The Dark Knight. I'm not sure why you think that Christopher Nolan's films involve nothing but exposition. In fact, most of his films find their true emotional resonance within the thematic backbone of the film rather than the plot. Have you seen Memento or The Prestige? Both of which have very complex and non-linear narratives that while requiring some thought and possibly explanation, are deeply rooted in the themes they tackle rather than the actual plot. Memento dealt with themes of needing something to drive you, as did the Prestige. The theme of obsession with an ideal or goal is a common thread within Nolan's films and I dare you to tell me it wasn't prevelant in Batman Begins or The Dark Knight. You may not have cared for The Dark Knight much, but you can't argue the film's merits. I think that is the main problem with film criticism these days is that people confuse the idea of enjoying a film with the quality of a film. Any film on earth can be picked apart to death and you can find flaws with any of them. However, it all really boils down to what works for you. Citizen Kane may be considered the greatest film of all time by a lot of people, but that doesn't mean everyone likes it. Likewise, just because you don't like something doesn't mean it isn't good. Bottom line, bringing up Christopher Nolan in a debate about the inclusion of Bubastis in Watchmen is a clear indicator of several things. You either didn't like The Dark Knight or simply preferred Watchmen to it. Either way, I am getting tired of these Watchmen vs TDK arguments. How is one like the other? Trying to compare the two is apples and oranges. It's pointless and idiotic.