Creator Backlash/Writer Revolt: A lot of people involved weren't happy with how the story was going and this resulted in quite a few changes in direction.
Fan-favorite writer Tom DeFalco was often said to be particularly displeased with killing off Doc Ock, and he unfortunately wound up being required to write that issue. First chance he got after the saga, however, he brought Ock back. He also didn't like Gaunt and seemed to try to kill him off as quickly as possible. Similarly, regarding both of them, when doing the alternate universe miniseries, he just opted to have Ock survive his encounter with Kaine and have Harry come back without the idea of him being Gaunt.
Executive Meddling: The series was prolonged due to sales, causing the quality to take a dive. The Clone Saga had the misfortune of debuting during a regime change in Marvel's editorial staff; the high-earners (Editor-in-chiefs who managed to boost sales during the comics recession) were kept on; losers found themselves demoted or downsized. This Glengarry Glen Ross approach put extra pressure on editors to prolong the Clone Saga event, even if it meant dropping meaningless hints and clues to tantalize readers. Consequently, several "back door" escape routes were proposed and rejected. (See below) The end result was that the Clone Saga, intended to dispel the dark, brooding tone of the 90's Spidey books and go "back to basics", ended up becoming the darkest and most impenetrable story yet.
Not to mention that, like One More Day, it was an attempt to return to the days when Spider-Man was single.
The famous Life of Reilly details what went on behind the scenes, but long story short, what prolonged it was greed (despite the criticisms and mocking it gets, it was making Marvel money), attempts to recreate the success of another storyline from the same time (hence the "Maximum Clonage: Alpha and Omega" one-shots and the Scarlet Spider titles for a few months), trouble behind the scenes over where to go with the story, and not wanting the finale to compete with the Onslaught storyline.
Executive Veto: This happened enough times that it almost belongs under Executive Meddling. Among the story threads that were shot down: Ben adopting Peter's identity after the latter passed away (leaving the Spider-canon more or less the same), one Spider-Man dying in an explosion while the surviving one loses his memory, and (wait for it...) having Mephisto erase the whole thing via a Cosmic Retcon.
Fan Nickname: Spider-Ben for Ben Reilly when he takes over as Spider-Man.
Lying Creator: Some fans think this of the "director's cut" miniseries; it's hard to write a story as "originally intended" when you had a bunch of separate people having different intentions.
Old Shame: Quite a few people involved aren't fond of the saga themselves.
What Could Have Been: A lot. They can all be read on the Life Of Reilly article. A few notable ones, some of which were uses in the 2009-2010 "director's cut":
At one point no-one was the clone, and in fact Peter and Ben were the same person caught in a Stable Time Loop. When this went against Marvel time travel rules, it was decided that someone was needed who could plausibly ignore said rules. So Scrier was going to be Mephisto, and he was going to trick Peter Parker into going back in time and becoming Ben Reilly in order to gain the soul of Judas Traveller, who was going to be a Fallen Angel. This was nixed for many of the same complaints againstOne More Day.
Another was that the character Gaunt would be the mastermind, with the idea being that the real mastermind was coming back from the dead inside Gaunt's costume, although they weren't initially sure who Gaunt would be. Eventually they decided Gaunt's identity would've been Harry Osborn, but this was felt to be too much like a previous story where Harry posthumously made robotic duplicates of Peter's parents. This led to them going back to the drawing board and making the mastermind not be Gaunt, which drew out the story even more. The mastermind became Norman Osborn, while Gaunt eventually turned out to be Mendel Stromm.
The recent "director's cut" mini-series used the idea of Harry as the mastermind, albeit having Harry faked his death rather than actually dying and coming back.
The Final Adventure mini was supposed to retire Peter as a superhero and MJ give birth to their daughter. Before the final issue was completed, everyone involved knew Peter would resume being Spider-Man, so Marvel wanted the mini to end with MJ having a miscarriage instead. Editor Tom Brevoort refused, the Life Of Reilly even quoting him as saying, "There's no way in hell that I'm going down in history as the man who killed Spider-Man's baby."
Word of God: The Life Of Reilly article features commentary from people involved in the Clone Saga, including revealing bits that didn't make it into the story such as Kaine's costume featuring a Life-support system and as a result of the defects in him, his Psychic Powers and Mark of Kaine were just amped up versions of Spidey's Spider-Sense and Wall-clinging abilities.
Writing by the Seat of Your Pants: Looking behind-the-scenes, it becomes clear that no-one really knew what was going to happen with the story. Or that someone did, but didn't let the others know; a "too many cooks spoiled the soup" argument is easy to make.
Especially regarding Judas Traveler. It's since been revealed that no one on the staff had any idea what his backstory and motivations were.