I think the main storyline of Pentangeli would have been the same. However, what we would see with Clemenza in it, would be more the tragic story of an anti-hero: Clemenza helped Vito in his early crime career and was a trusted and loyal friend and capo, he became a father figure for young Michael. Imagine Clemenza in the courtroom, looking at his brother, becoming nervous, etc. Imagine if we saw Tom talking to Clemenza instead of Pentangeli about history. Michael's guilt woul be heavier, his soul even darker.