Cora wasn’t exactly a picture of mental health and happiness. She was a very angry, arrogant girl.
I get what you’re saying and I do think there is a magical connection between Emma and Regina in that one is dark and one is light and that’s pretty powerful but I don’t think it is something Rumple wants to forestall for some end game. Afterall, he was perfectly fine with the Wraith taking her soul and having her effectively die.
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"He was a lot of things to me" "The only conclusion was love"