This effect can happen a lot with online fanfiction as well; any particularly well-executed fanfic that takes source material in a new direction is likely to spawn a horde of imitators, rapidly turning the original author's new and innovative take on the source material into a tired cliche. With fanfics that are Long Runners or suffer from Schedule Slip a story can actually go from innovative to cliched before the author is even done writing it.
A lot of older fanfic suffers from this, especially in large, well-trafficked forums like Harry Potter, when a fic that invented or popularised a popular piece of fanon is examined in light of what went after.
Likewise, the old apas and zines seem quaint and silly in comparison to the internet. Many younger fanfic writers never heard of the days when it was incredible to get four or five novel-length fanfics circulated in a year.
This is a notable problem with many old Redwall fics, particularly The Urthblood Saga, that deals with the theme of "noble vermin". When these fics where written back in the late 90's/early 2000's, the concept of including good foxes, rats and weasels in a story based on a series that is so strictly black-and-white was fresh and challenging. Nowadays however, it's rare to find a fic that doesn't include it, or that plays the Always Chaotic Evil mantra from the official books straight.
A vast majority of Ranma ½ fanfics written after 1998 or so were built almost entirely upon Fanon established in earlier works by notable authors; the absolute worst case of this being the Flanderization of Akane into a brutally violent, abusive raging bitch with a hair trigger and no rationality whatsoever—which was given legitimacy in the very dark "The Bitter End", a story which painted a darker picture of the Ranmaverse and reconstructed this portrayal, with a Freudian Excuse, in the process. After TBE, "psychotic Akane" became one of the biggest cliches in Ranma fanfiction to the point that most people roll their eyes and groan when they see a story going in that direction.
Also, the amusing parody crossover Sailor Ranko spawned an entire subgenre of Ranma fanfiction.
Harry Potter has inspired one of the most prolific fanficcer communities ever. As a result, tons of clichés have formed over the years. A modern reader might find a fic way back from 2002, filled with clichés and not realize those he's reading were the first fics to use some of those ideas.
Of course, before that, the standard portrayal was even further from canon, most fanfics showed her as timid and insecure.
There are numerous cases of fanfics written early in the life of the fandom that were well-known and popular for being the first to utilize certain ideas, and now come across as rather non-notable in light of everything produced since then:
Cupcakes was the fist major MLP Dark Fic with copious amounts of Gorn, and was generally considered the most disturbing thing in the fandom when it came out. Ever since then, there have been an awful lot of grimdark imitators that make Cupcakes look mundane in comparison (Example: Sweet Apple Massacre) and now some people don't find it as scary.
Fallout Equestria was the first epic-scale Door Stopper fanfic to gain real popularity in the fandom. Had it been written after the first few seasons, it would have simply been one among many other similar stories. It still has a dedicated fanbase within the larger fandom, but it's not nearly as widely viewed as groundbreaking in the way it was when it first came out.
A Trekkie's Tale. Being the source of the term Mary Sue, people who seek the story out may be disappointed to find that it's extremely short, and a quite basic parody. Then you consider that it was written in the early '70s, when even the idea of fanfic itself was in its infancy.
The fact that it was parodying the very things that make up Mary Sue characters, which were already becoming common in Star Trek fanfiction back then.
Kikyo-Bashing in InuYasha was once considered somewhat of a comedic (or just refreshing) take on the character. Nowadays, a lot of people are just flat out tired of Kikyo-Bashing, some even going so far to see it as "unnecessary" or "annoying".
There are a whole raft of Battlestar Galactica - Stargate SG-1 fics out there in which the Colonials are all portrayed as religious fanatic nutjobs who are offended... OFFENDED, I tell you... that the people of Earth don't immediately throw away their false religions and their stupid ideas of freedom and democracy and join with their ancestral brothers in the worship of the Gods of Kobol and step in line with the military dictatorship that runs the 12 Colonies. It all stems back to one rather well-done story that has since been endlessly copied, in which the Colonials are religious, but they aren't quite that level of fanatic.