I agree. I was watching a rerun from the first season and they mention christopher working for a startup tech company in california like logan was supposed to in season 7 but other than some minor parallels, they are really two different people. Rory rejected Jess in season 6 because she was in love with Logan. Lorelai would not have rejected Luke for christopher.
Also, I see Jess more like a friend to rory who gives advice when he is around but she never really seeks it from him. He just shows up, kind of like christopher. While Rory seeks out logan for advice and to vent. Logan is more like Luke for Rory in my opinion.