I don't think either was a bad idea. Gwen was a boring character (and just calling her a character is a bit generous)... accept the times when she was kind of a bitch.
The original clone story was a really good story.
If I have to chose, I would say the cloning.
If I can think three-dimensionally, I would say the real mistake was ignoring the end of the Clone story, when Peter realized he had moved on past Gwen. Still cared for her, wasn't in love with her anymore.
This lingering idea that he is hung up on Gwen that pops up every now and then is way more annoying.
Peter being 'hung up on Gwen' was always countered in those stories by him frequently reminding himself how much stronger his love for MJ is though.
Even in Clone Conspiracy, when the alleged 'real Gwen''s soul was placed in a cloned body, she makes it clear to Peter she always feared she would lose him to Mary Jane. She knew Peter cared about MJ more.