I'm with you. I have a lot of fond memories of the Clone Saga, and yes there are very patchy areas, mostly everything in between Aunt May's death and Ben taking over, but everything before and after then is pretty pacy, intriguing, emotional and action-packed...and, as I've said, most of the saga does gets a pretty rosey resolution in Spider-Girl.
Bor, did you ever manage to read the "Real Clone Saga" mini-series from Tom D and Howard Mackie which Marvel published during the BND era? Did you think it was an improvement?