I know that with the new 4.3 2D stuff, when I create a project, I have an option to use 2D or 3D. When I set to 2D, it sets up my project for 3D. I know that I can change the settings, so it is only a minor annoyance, but is there any way to fix this?
I have solved my own problem. To fix this, just change to 2D mode, then create a new scene. Unity will set up the orthnographic camera and stuff for you.