IMHO if you'll be swapping out your wheels (especially if going bigger) the limited flares look better as they're a bit wider. Not really an advantage...probably more of a preference. It really all depends on what type of setup you'll ultimately want to end up with.
You don't have any more options for tire size with the Limited flares. They are just a little wider so if you get wider tires, they won't spray as much mud down the side of the truck.