I think the most interesting thing they could do with this (and many will disagree), is have a Peter and a Gwen clone living happliy together in some small town. They have regular jobs where they work at a lab, they have kids, they have regular people worries. The clone Peter has no powers, having gotten rid of them years ago. They are also both aware that they are clones, one of the projects of Miles Warren that managed to escape during any of the Spider-Man dust ups that they have had.
When original Peter meets them, it all comes crashing in as to what might have been if he had made different choices. Panals of Peter playing with kids that have his face but Gwen's eyes for example. I think they would be an interesting method of exploring what it is Peter is looking for in life, as oftentimes it seems like he is simply just going from one encounter to the next.
Enter the Jackel. He has tracked down his wayard clones and it is up to Peter to rescue them and keep them safe. I also think it would be interesting to have the Jackel clone some of Peter's enemies, including the Green Goblin and toss Gwen off the bridge again, this time of course Peter catches her. Having to protect clone Peter might be interesting in that he would see just how much confidence and how much of his own self-image is wrapped up in being Spider-Man. Lots of times you see Peter thinking of Spider-Man and himself as two seperate entities, this would be another method to help bridge that gap.
Just some thoughts on it, I have no doubt there are people that would detest this and will probably tear it apart. But I was trying to go with the spirit of the thread