Why did Red John "mark" Lisbon? I mean he chopped off Sophie Millers head and she was very close to Jane. And obviously he killed Janes whole family so why the soft spot for Lisbon?
To me, marking Lisbon means Red John claimed her as his own or his territory like a dog pissing in a specific spot.
Red John loved/loves Jane as Styles said. He ultimately wanted Jane to join him and thats why he kept Jane alive all these years. Over the years Red John only "worked" through Jane and seemed to have no other agenda rather than Jane. Macalister exhibited no signs of care or love for Jane in the church. He didn't ask him to join him or anything like that either. I believe Red John felt it would be more painful for him to actually steal Lisbon away from Jane. This Pike stuff raises too many Red Flags for me to think its just a little story line.