Feel compelled to weigh in here. The reason that Michael decided to move on from his relationship with Kay was because he was no longer the same man that she fell in love with. If you remember at the wedding, he says, "That's my family. It's not me." Well, after killing Sollozzo and McCluskey, it IS him. He makes the assumption that Kay, being from a different world, would no longer want to be with him.

When he falls in love with Appollonia, it is a completely different kind of love. He loved Kay for her intelligence and independence, as well as his physical attraction to her (which was partially based on her looking "different"). His relationship with Appollonia was based her looks, her simpleness and her understanding of the man he had become and the life he had embraced.

When he gets back together with Kay, he explains to her that, if they do marry, their relationship will be changed. It will no longer be a partnership, as it used to be. He can't confide in her as he once did.

She accepts those rules, thinking that their life will go back to "normal" when the Corleone Family goes legitimate. When that doesn't happen as Michael promised, her anger and resentment build and their marriage is destroyed.

Appollonia would never have expected to be a partner. For the man that Michael became, she may have made a better wife in that she would have been much more complacent in that role of obedient wife.