Even Spider-Man: The Animated Series openly hated the Clone Saga. The Clone Saga was one of the most controversial Spider-Man stories ever told. It ran from 1994 through to 1996, and featured a frankly staggering number of retcons and pivots. The whole storyline was intended to simplify Spider-Man's mythology, but it accomplished the exact opposite.
Viewed in retrospect, the whole arc was ill-considered. It introduced characters such as Judas Traveller and Kaine, who were ill-defined and poorly thought through. Matters were compounded when the entire comic book industry hit rocky times in the '90s, and Marvel came shockingly close to bankruptcy. With the company in desperate turmoil, the writers lacked any real editorial support, and they were under pressure to extend the storyline because of strong sales performance. At its height, the Clone Saga featured a strange retcon that revealed Peter Parker was actually a clone; he was replaced by Ben Reilly, the man who had always been thought to be a clone.
The fifth season of Spider-Man: The Animated Series culminated in a story inspired by the Clone Saga, and it took a very different approach. Writers James Krieg, Mark Hoffmeier, and John Semper took their version of Peter Parker to an alternate universe, where something similar to the Clone Saga had taken place; that universe's Peter Parker had been driven insane by the experience and had been turned into a monstrous supervillain after merging with the Carnage symbiote. But the writers made no secret of their disdain for the plot; the story even kicked off in an episode entitled "I Really, Really Hate Clones." When Peter learned of the alt-universe clone story, his response seemed to speak for the writers; "This is beginning to sound like a bad comic book plot."
John Semper clearly felt the Clone Saga was too important a part of the Spider-Man mythos to ignore completely, especially given it was performing so well in terms of sales. At the same time, though, he was afforded an unusual amount of independence in writing Spider-Man: The Animated Series, allowing him to take such a distinctive approach - and make what, in hindsight, seems to be a clear commentary on the quality of the story in the comics. By this time, the chaos in Marvel meant nobody was really paying any attention to the show; everybody was too busy trying to keep the company afloat.
Modern comic book readers generally agree with Semper's assessment. Looking back, the Clone Saga was indeed a bad comic book plot, a story that became so convoluted even its own writers struggled to keep track. The Ben Reilly retcon was undone, and for decades Spider-Man comics avoided clones altogether. In-universe, even Peter Parker has uttered those words; "I really, really hate clones."