The Clone Saga was just a bad idea period. The premise was flawed from the start. According to their logic, Marvel thought everyone reading the book would just say "oh, the character we've followed since 1975 really isn't Peter Parker. He's just a clone of the real one. Cool!" They deserved every bit of flak they've received for trying to palm off such a lame story. They were pretty much saying that SPECTACULAR SPIDER-MAN, WEB OF SPIDER-MAN, AND SPIDER-MAN never featured the true Peter Parker. To this day it amazes me (no pun intended) that the story ever got approved. To make matters worse, the idea originated with the lguy who came up with the teen Tony Stark fiasco in Iron Man around the same time.....TERRY KAVANAGH.
Holy Crap! Terry "the man who gave us FACADE" Kavanagh was also behind "Teen Tony" as well? Geez, it was bad enough that Marvel took him seriously regarding the Clone Saga, considering how this was the guy who killed off Lance Bannon via a "mystery" villain whose identity, to this day, has never been revealed, or cared about.
If Marvel really wanted Peter to be single back then, they should've just knocked MJ off in 93 or 94 or simply had the couple break up. Had they done it, she would've been out of the book for over 10 years by now and we wouldn't now be facing the "One More Day" fiasco.
Or they could have gone with Tom DeFalco's original idea for the 1987 ASM Annual, where instead of getting married, either Mary Jane leaves Peter at the altar after getting cold feet, or Peter is late to the wedding because he gets caught in the middle of a superhero battle and when he does show up, the wedding has been called off (can't recall which of those scenarios he wanted to use). I'm sure that IF "One More Day" a.k.a "Maximum Marriage" (props to farmernudie for that one) erases the marriage, Joe Q will respond to the criticism that it would erase 20 years worth of stories by saying, "Oh no, those stories still count. It's just, because the new reality had Peter and Mary Jane not married, they decided to have a "trial marriage" and live together before tying the knot. But his life as Spider-Man, and especially what happened during Civil War and Black in Black, got in the way of their happiness." And if that's the case, I guess that means that whole baby May incident under this new continuity would mean that, since Peter and MJ weren't married, the baby would've been born out of wedlock. Yeah, I'm sure parents who thought Spider-Man was supposed to be kid friendly will "love" that move, especially since [BLACKOUT]Sins Past[/BLACKOUT] is still fresh.
As for me, if I had to reset continuity, I'd probably not have ASM #28 be the graduation issue and bring in Harry, Gwen, and Mary Jane while Peter is still in High School. Course, you couldn't have Flash going to Vietnam or Peter moving in with Harry subplots but certain things could be the same while certain things would probably be dramatically different. Liz Allen could leave the title in ASM #28 due to moving somewhere else, allowing Gwen to come into the picture. The actual "Peter graduates from high school" story would appear in ASM #100 to act as a milestone event, although it probably get rid of the set-up for the whole "Six Armed Spidey" for later. Gwen, after the death of her father, instead of going to college, goes to the police academy to follow in her father's footsteps in the hopes of bringing down Spider-Man. Flash would then join the army in the new ASM #100 issue as well. Unlike as depicted in "Parallel Lives" Mary Jane didn't always know but gradually put two and two together to figure out Peter was Spider-Man--as anyone observant would. Either this or have it so ASM #195 was not the "Peter almost graduates from college" issue. Basically, it would have to be something along the lines that Peter stays in a high school/college setting for as long as possible. Of course, doing so would probably cause all kinds of headaches, especially if it was a hard reboot.
One thing I'd definately reset would be Venom's origin, especially Eddie Brock being the host. I'm in agreement with Madgoblin's Venom column that Lance Bannon would've been a much better choice, considering how he and Peter were already rivals, were in the same profession, had opposite personalities, and that Lance was also a developed character who had sympathetic traits along with his being an ass. Plus, the fact that he was involved with Amy Powell would've likewise given a tragic element, and we never would have gotten the "Who is FACADE?" mess.