Both institutions are excellent and both doctors seem qualified (I am not personally familiar with either of them). Emory is a medical school/teaching hospital which, IMHO, is always a plus. I suspect that the "Mayo Mystique" is more due to the reputation of the parent institution in Minnesota than any particular attributes of the Jacksonville site.
Dr. Mehrdad Alemozaffar has trained at two of the best places for bladder cancer....Boston and USC. If the Emory location is as convenient for you and since you are already familiar with the set up and procedures, and if you feel personally comfortable with Dr. Mehrdad Alemozaffar, there would be no reason to switch. I think you would be in good hands!
However, if you are in any way unhappy with the current situation, this would be the time to switch.
Good luck to you
Sara Anne