Said it before, I'll say it again: All they had to do to salvage (not save, way past that point, at this point) the Clone Saga is make Peter the real thing and have him say "I'm hanging up the mask to be with my wife and kid-to-be. Ben, the mask is yours, if you want it. You may be a clone, but you're Spider-Man in every way that counts.".
There: New beginning, new cast. No intelligence-insulting "twist", no ass-pull retcon to fix it.