I don't see what the identity of the main character has to do with the quality of the storytelling.
Really? You don't see how exchanging the title character in a continuing series with his worst enemy could put some people off?
The quality of the storytelling isn't really the issue for me in this particular case, the identity of the main character IS. I've been reading about Peter Parker's life as Spider-Man for over 40 years. I like Pete, he kinda reminds me of me. I like Pete as Spidey, he makes me think any picked-on kid can end up a hero. That's what I buy Spider-Man to read about. Otto Octavius does NOT remind me of me - I have nothing in common with a rich, evil megalomaniac. They could have done the greatest "quality" story in Marvel history in this run (which they didn't), but since it wasn't Peter Parker being Spidey, I wouldn't have cared.
It was obviously a temporary story. Seeing the drama of the switch, if well-written, should overcome everything else. It's still in the same universe and relies on the past history that led to that point. Now whether it was good writing or not, I don't know, since I didn't read it. But it's not inherently bad.