I think Brain is a real character. However I believe the brain is metaphorical for brendan's rational/logical side and brendan is passion/emotion in his pursuit of Em. This metaphor only works specifically in their conversations; as in, they are both separate characters, when not in the room together, performing tasks independently. When in the room together they take on these rational/logical and emotional roles.
I didn't read all of the posts, but I read enough of it, and I agree.
I think the Brain is a real character, but he's also a literary tool. I think only with the advent of post-modern films did we start to question the legitimacy of whether a character is real or not. There are so many movies like Fight Club, Identity, Secret Window, etc. However, I feel like Brick is in a genre of films that predates these kinds of films, where when you have a character it is used as a literary tool rather than a plot technique.
For example, look at a book like Crime and Punishment. Most of those characters are foils of Raskolnikov, but they are definitely real characters in the book. Or look through any good book, real characters used to explain the main character, but they certainly are real.
And of course the shots of the Brain and the his name even does heavily suggest that he's a metaphor for that other side of Brendan (no doubt about that), but I would like to think that metaphors can be real characters as they are in books. And that at the core of Brick is a great script.