Residents at fellow-laden programs will experience a dilution of case complexity that would not occur if the fellowship programs were not in their institutions. I don't care what program directors tell you to the contrary. Sagely advice was given many years ago on this forum that spoke to this idea and it is advice that has proven to be true in my experience as I have transitioned into fellowship.
It's an important question that you need to ask yourself in applying to residencies: is pedigree more important to me than my clinical exposure? I don't want to make the two sound to be mutually exclusive but there are some (if not many) programs considered to be elite that offer only marginal clinical experience during the subspecialty months (due to the demands of getting fellows good cases).