This gets a root at what the whole show is about. The major theme of Fringe is exploring the impact of choices and how we impact the people we love/vice versa. The show does this through the Alternate Universe and also the Peter-less timeline. As the poster above mentioned, it's much like The Firefly. His absence effected little things, which in turn effected other things. For example, without Peter to console Olivia in the white tulip field (Subject 13), she was unable to reconcile her issues with her father. That's shy she killed her father in this timeline. That's why Olivia/Rachel moved in with Nina. That probably set Rachel's life on a different course, much like Olivia's.