Popular movies get discussed to death and over-mis-interpreted to the point where just the mention of it causes a mental effort to ignore the assumed sycophantic rambling that's to follow.
Popularity ruins perceived quality by the nature of media to seize upon it and, as someone else said in a slightly different context above, squeeze every last cent of profit out of the opportunity that's presented by it's popularity.
Technically it doesn't affect the quality, but it adds a thick layer of media slime that can take years to dry up and fall off.
Lastly, popularity and quality are two scales that have interesting intersections. It's a concept I'd actually like to investigate further.
Kojima and the Metal Gear series.
Another mechanism is flanderization, in which writers simplify characters or other aspects of the show for various reasons, mostly laziness and to conform to expectations the audience develops about how characters should act. Characters with depth become shallow shadows of their past selves as one aspect of their personality starts to dominate the others. When characters are driven by audience expectations instead of the writer's internal muse, they become soulless and predictable.
Another is overdeveloping the setting. Throwaway lines in earlier media get needlessly turned into developed storylines. It leaves less to the imagination. This is often related to the first mechanism I mention; the writers squeezing all the juice out of the earlier media.