IMO, Jess and Rory always had poor timing. When they were together in high school, he was too messed up and she was too skittish to be honest with him. It was in season 4 when he returned to Stars Hollow for his mother's wedding that he asked her to run away with him and she emphatically said no. I don't blame her, he wasn't in a good place. When he returned 2 years later she was involved with Logan. Jess and Rory, at that time, could have started something, but for Logan. She was the one who actually treated him disrespectfully at that time.
Do we know that she never looked back fondly on her relationship with Jess? In the revival they seem to be friends.