Jamie - It is likely that theatre experience compounded the problem as it does make for a much more intense experience of any film. But Nemo starts with a baby loosing their entire family and goes down hill from there, including themes about AA meetings (WHY???) and a crazed dentist (WHY??), none of these are themes my 2.5yr old needed to experience. After 9 months of obsessing and panic in public places, Nemo finally ended up being the only film my DD would watch for a while too (the final stage of her obsession and working through it). But I still think it is the classic example of "kids" films being made for adults.
I did not like the beginning where the mom and siblings are lost either. What I did was not tell my daughter what had happened. She was more worried about the scary looking baracuda. After about 30 times watching the movie, she figured out what the beginning meant. I didn't like having to confront the death question before age 3, especially one involving a parent.
Old Dismey movies bother me even more though. They over play the good vs evil theme, too many wicked step mothers and even the idea that happiness for women is all about marrying some prince. I think some of the old black and white non-animated movies had better themes in them for children.
My daughter's sensitivities in movies seemed to be scenes involving what appeared like conflict between characters. Although maybe it was just the raised voices bothering her. She tends not to like louder type people as well, which is the same for me. My family are soft spoken.
At 4, she was going through movies to find one she had not watched and came across "Rocky". I warned her she probably would not like it and told her it was about fighting. She was willing to try it out and she loved it and then I got to see Rocky over and over. I guess the soft spoken characters made the movie ok for her. I wish I could remember the kid's movie she refused to watch at this time which I thought was mild.
Before having a child, I intended to be fairly open as to what I would let them watch. This was how I was raised. I did not however intend to allow movies I felt were just plain stupid like horror films. Then again, I also feel exposure to tv and music should be held back as long as possible anyway. This I feel is particularly critical in children at risk of having accelerated learning.