I usually cheer for the bad guy, unless the good guy is a badass (i.e. James Bond). Then I cheer for the good guy.
I used to always think about a movie when I was watching it...but that ruined a lot of good movies because I noticed flaws and other things that didn't make sense. So, now I just sit back and watch and more movies are good this way. This means that I generally root for the guy the movie makes most sympathetic.
It depends on the bad guy really. Some bad guys really are not bad simply misunderstood and then there are the crazies. If they are in that grouping I root for them. Then it depends on the good guy, hate most good guys who are Naive and bitchy. I can root for some innocent characters but only if the innocence is in the same manner as Tarzan, raised bye the wild and all.
Movies are too formulaic. I just try to figure out who the shapeshifter* is. A shapeshifter is an archetypal character whose primary essence either is in doubt ("is she lying to me?") or changes suddenly ("I thought you were a man!"). In some cases the hero is a shapeshifter, sometimes the shapeshifting qualities of a character are a central part of the story--but often suddenly in the climax you learn that someone isn't what he or she seems to be, such as when a double agent is revealed. the "shapeshifter" is a central part of storytelling, along with the hero, the mentor, the threshold guardian, the herald, and the trickster, etc., In star wars, obviously Darth Vader was the shapeshifter. So was Leia, when she was revealed to be Luke's sister. Han Solo was also a shapeshifter, since you didn't know if he would help the Alliance or not until the very end.
Aw yes my English classes classes are coming back to me now. Fun times. I had to give a presentation once on the formula of a story. To illustrate my point because it was a two part presentation I had the rest of my class give me a topic and items that were related to said topic. I then made a short epic comic. The adventures of B-Ball and Shoe.
I gravitate towards anti-heroes and sympathetic villains -- the more black and white the movie paints its characters the less I care.
