I think they should have had Ellie give Joel the antibiotic, lay down and go to sleep, then have Joel wake up to find Ellie gone. He would start his part of the level where he leaves the house to search for her and finds the hunters and interrigates them.
Then fade to black, title, "Earlier that day", and Ellie wakes up and hears the hunters outside and starts the level where she leads them away from Joel.
I would have liked that better, where for a short time I didn't know where she was or what happened to her.
Naw, none of that "earlier that day" stuff. It was perfect the way it was. Also, it would take away the effect in the ending.