Question: I'm a little confused about Greta's death. Was it from eating too much or from her eating what was not good for her?
Answer: In the VHS version, Freddy cut open her stomach and was feeding her own intestines. That's why when he cut open the doll on the high chair tray Greta was wincing and squirming as Freddy had just cut her stomach open. I guess you could say that that doll on the high chair tray was like a voodoo doll of Greta so whatever Freddy did to it happened to Greta too. Eventually, Freddy caused Greta to choke on her own intestines which caused her to choke to death in the real world.
Question: Why did Louis kill Church at the end? He only planned on killing Gage if he came back like Timmy Baterman did, and he could have just walked in after distracting Church with the meat.
Chosen answer: Church's behavior had changed after being buried. He was now violent (and working with Gage) and needed to be put down before killing anyone.
Question: After the gene-swapping sequence, why was Bartok placed in observation? Also, what was that food they gave him?
Chosen answer: Obviously, he was kept alive so he could be studied, which was a nasty twist on the fact that he kept the dog alive, and suffering, for so long. As far as the food, there is no way to know what it was. Probably some kind of bland mush.
Question: Do the sewers of New York really fill up with toxic waste every night as stated in the movie, or was this just for the purpose of the plot?
Question: Why does Jamie calling him uncle stop him? That and why honor her request to see his face?
Answer: Sorry about that and thank you.
Answer: The question was more-or-less answered in a previous question, so I'll copy part of my answer here: Director Dominique Othenin-Girard made the puzzling decision to try and humanize Michael in this film by showing he still had some traces of emotion that could be momentarily reached. Thus when Jamie talks to him, he briefly recovers his humanity, takes off his mask and sheds a single tear. Basically, Othenin-Girard felt it made Michael scarier by showing his humanity could be momentarily "reached." Of course, it really doesn't make sense and contradicts the other films... but it was just a decision the director made.
Answer: Her death was from Freddy overfeeding her while in the real world she choked to death.