Logan Is the Father
This is the most obvious answer. Rory is sleeping with Logan throughout A Year in the Life and only breaks up with him for good in the "Fall" episode. Consider an interview that Amy Sherman-Palladino gave to Entertainment Weekly days before the new series premiered. On the topic of Logan, she says, "We wanted Rory to date her father. Every girl has a father issue, and Logan was Christopher. Logan was charming, smart, and not quite the dependable soul that you need. Or, at that time, was not the great dependable soul."
It would be a full-circle moment for Rory to become pregnant with Logan's child, as Lorelai has become pregnant with Christopher's baby.