Lets make this very simple.

Green:  Sherrif Thomas McAllister is Red John. The Red John story is over, and we are left with a lot of loose ends (eventhough some are answered, like Red Johns phobia, tyger tyger burning bright, etc.)

Red:  Red for Red John, he is still out there and will blow everyones mind in the finale episode (eventhough Heller said the Red John story is officially over now).