At this point in time, I have read most but not yet all of it. Albeit I do know some of the story elements from the issues I haven't yet read.
I can see why it was disliked, for one thing, at the time it started, it would have been very hard to get the full story, as the overall storyline jumps from title to title and there are often even multiple multi-part story arcs running at the same time.
Secondly, this is something that affected the Spider-Man titles for years. So, plenty of people must have gotten tired of it at some point.
Then of course there was the revelation that Peter is the real clone and not Ben.
But would it have worked as its own isolated story? I think it would have considering how popular many of the big players from the Clone Saga are.
Also, there was a miniseries from the 2009 that redid the whole Clone Saga story. It shortened it and didn't kill of Ben Reilly and baby May. IIRC, Doc Ock survived as well in the 2009 version, but I could be misremembering. At the end, Ben Reilly eventually gets back on the road, basically back to where he started at the beginning of the story, I guess.